% LiteralHTML:
% LiteralHTML:     <H2><center>Research and Publications that make use of PETSc</center></H2>
% LiteralHTML:
% LiteralHTML:  <a name="nano"><H3><center>Nano-simulations</center></H3>
% LiteralHTML:

@article{Rupp:2016:PIS:2988256.2907944,
 author = {Rupp, Karl and Weinbub, Josef and J\"{u}ngel, Ansgar and Grasser, Tibor},
 title = {Pipelined Iterative Solvers with Kernel Fusion for Graphics Processing Units},
 journal = {ACM Trans. Math. Softw.},
 issue_date = {September 2016},
 volume = {43},
 number = {2},
 month = aug,
 year = {2016},
 issn = {0098-3500},
 pages = {11:1--11:27},
 articleno = {11},
 numpages = {27},
 url = {http://doi.acm.org/10.1145/2907944},
 doi = {10.1145/2907944},
 acmid = {2907944},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {BiCGStab method, CUDA, GMRES method, GPU, Iterative solvers, OpenCL, conjugate gradient method},
}
@article{dalcin2011parallel,
  title={Parallel distributed computing using python},
  author={Dalcin, Lisandro D and Paz, Rodrigo R and Kler, Pablo A and Cosimo, Alejandro},
  journal={Advances in Water Resources},
  volume={34},
  number={9},
  pages={1124--1139},
  year={2011},
  publisher={Elsevier}
}
@article{MendezPongaOrtiz2018,
  title   = {Diffusive molecular dynamics simulations of lithiation of silicon nanopillars},
  author  = {JP Mendez and M Ponga and M Ortiz},
  journal = {Journal of the Mechanics and Physics of Solids},
  year    = {2018},
}
@techreport{morgan2020evaluation,
  title={Evaluation of {PETS}c on a Heterogeneous Architecture, the {OLCF} {S}ummit System: Part 1: Vector Node Performance},
  author={Morgan, Hannah Mairs and Mills, Richard Tran and Smith, Barry},
  year={2020},
  institution={Argonne National Laboratory},
  url="https://publications.anl.gov/anlpubs/2020/04/159190.pdf"
}
@techreport{pdeconstrainedspectraladjoints,
  title       = {PDE constrained optimization, error estimation and control with spectral elements using PETSc and TAO},
  author      = {Oana Marin and Emil Constantinescu and Barry Smith},
  type        = {Preprint},
  number      = {ANL/MCS-P9031-1117},
  institution = {ANL},
  month       = {November},
  year        = {2017}
}
@INPROCEEDINGS{asc2013,
  author = "S. Abhyankar and B. F. Smith and E. Constantinescu",
  title  = "Evaluation of overlapping restricted additive Schwarz preconditioning for parallel solution of very large power flow problems",
  booktitle =  "HiPCNA-PG’13",
  year =  2013
}
@INPROCEEDINGS{as2013,
  author = "S. Abhyankar and B. F. Smith",
  title  = "{PETSc:} An Advanced Math and Computing Framework for Rapidly Developing Parallel Smart Grid Applications",
  booktitle =  "Proceedings of the IEEE PES General Meeting",
  year =  2013
}
@techreport{tspaper,
  title       = {{PETSc/TS}: A Modern Scalable {DAE/ODE} Solver Library},
  author      = {Shrirang Abhyankar and Jed Brown and Emil Constantinescu and Debojyoti Ghosh and Barry F. Smith},
  type        = {Preprint},
  number      = {ANL/MCS-P5061-0114},
  institution = {ANL},
  month       = {January},
  year        = {2014}
}
@TechReport{bb2008,
  author = "Tomasz Blachowicz and Bartlomiej Baron",
  title = "A graphical extension for the Windows version of the Parallel Finite Element Micromagnetics Package (MagParExt)",
  url = "http://arxiv.org/abs/0807.2655",
  year = 2008
}

@Article{jacvgv2008,
  author = "R. Y. Jaafar and  A Asenjo and O Chubykalo-Fesenko and M Vazquez and  E M Gonzalez and J L Vicent",
  title = "Field induced vortex dynamics in magnetic Ni nanotriangles",
  journal = "Nanotechnology",
  volume = 19,
  year = 2008,
  url = "http://dx.doi.org/10.1088/0957-4484/19/28/285717"
}

@Article{yjdwh2008,
  author = "Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He",
  title = "Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy",
  journal = "Journal of the Magnetics Society of Japan",
  volume = 32,
  year = 2008,
  pages = "50-53",
  url="http://www.jstage.jst.go.jp/article/msjmag/32/2_1/32_50/_article"
}


@Article{mtrtrsa2008,
  author = "D. Makarov and S. Tibus and  C. T. Rettner and T. Thomson and B. D. Terris and T. Schrefl and M. Albrecht",
  title = "Magnetic strip patterns induced by focused ion beam irradiation",
  journal = "J. Appl. Phys.",
  volume = 103,
  year = 2008,
  url = "http://dx.doi.org/10.1063/1.2894587"
}

@INPROCEEDINGS{tmrttsa2008,
 author = "S. Tibus and D. Makarov and C. T. Rettner and T. Thomson and B. D. Terris and T. Schrefl and M. Albrecht",
 title = "Patterning of magnetic films by focused ion beam irradiation",
  booktitle = "Intermag 2008 paper no. CM-05, submitted to IEEE Trans. Magn.",
 year = 2008
}

@article{yjdbh2007,
  author = "Lin Yuan and Jianju Jiang and Yongjiang di and Shaowei Bie and Huahui He",
  title = "Micromagnetic simulation of the magnetic dispersion angle and effective damping factor for the single-phase soft magnetic films",
  journal = "J. Magn. Magn. Mater.",
  Volume = 320,
  Number =  7,
  pages = "1393-1397",
  url ="http://dx.doi.org/10.1016/j.jmmm.2007.11.025"
}

@article{lxky2007,
  author = "DENG Lian-wen and HUANG Xiao-zhong and ZH0U Ke-sheng and YANG",
  title = "Micromagnetic simulation and experimental study on microwave permeability of nano-magnetic films",
  journal = "Transactions of Nonferrous Metals Society of China",
  year = 2007,
  pages = "756-759",
  url ="http://www.ysxbcn.com/icnfm2007/part2B/s0756.pdf"
}

@article{yjdwh2008a,
  author = "Lin Yuan and Jianjun Jiang and Gang Du and Zhongyou Wang and Huahui He",
  title = "Micromagnetic Simulation of Magnetic Particles with Surface Anisotropy",
  journal = "Journal of the Magnetics Society of Japan",
  Volume =  32,
  year = 2008,
  pages = "50-53",
  url = "http://dx.doi.org/10.3379/msjmag.32.50"
}

@article{lylw2007,
  author = "Ching-Ming Lee and L. X. Ye and J. M. Lee and Te-Ho Wu",
  title = "Micromagnetic study of magnetization reversal in patterned DyFeCo thin films",
  journal = "Phys. Stat. Sol.",
  volume =  204,
  Number =  12,
  pages =  "4049-4052",
  year = 2007,
  url = "http://dx.doi.org/10.1002/pssa.200777359"
}

@INPROCEEDINGS{sg2007,
  author = "Simon Greaves",
  title = "Micromagnetic Simulations of Magnetic Recording Media",
  booktitle = "High Performance Computing on Vector Systems 2007",
  url = "http://dx.doi.org/10.1007/978-3-540-74384-2_17"
}

@article{bsc2007,
  author = "Nadjib Benatmane and Werner Scholz and T.W. Clinton",
  title = "Magnetic Configurations and Phase Diagrams of sub-100 nm NiFe Nanorings",
  journal = "IEEE Trans. Magn.",
  volume = 43,
  year = 2007,
  pages =  "2884-2886",
  url = "http://dx.doi.org/10.1109/TMAG.2007.892867"
}

@article{ffbf,
  author = "T. Fischbacher and M. Franchin and G. Bordignon and H. Fangohr",
  title = "A Systematic Approach to Multiphysics Extensions of Finite-Element-Based Micromagnetic Simulations: Nmag.",
  journal = "IEEE Trans. Magn. Volume",
  Volume = 43,
  pages = "2896-2898",
  url = "http://dx.doi.org/10.1109/TMAG.2007.893843"
}

@inbook{dfssfs2006,
  author = "R. Dittrich and J. Fidler and D. Suess and W. Schol and H. Forster, T. Schrefl",
  chapter = "Computational Aspects of Micromagnetics",
  title = "The Science of Hysteresis",
  editor = " G. Bertotti and I. Mayergoyz",
  url = "http://books.elsevier.com/us/elsevier/us/subindex.asp?maintarget=&isbn=0124808743"
}

@inbook{fss,
  author = "J. Fidler and T. Schrefl and W. Scholz",
  chapter = "Computational Micromagnetics",
  title = "Handbook of Theoretical and Computational Nanotechnology",
  editor = "M. Rieth and W. Schommers",
  url = "http://www.amazon.com/gp/product/158883042X"
}

@inbook{shbsef,
  author = "Thomas Schrefl and Gino Hrkac and Simon Bance and Dieter Suess and Otmar Ertl and Josef Fidler",
  chapter = "Numerical Methods in Micromagnetics (Finite Element Method)",
  title = "Handbook of Magnetism and Advanced Magnetic Materials",
  editor = "Helmut Kronmueller and Stuart Parkin",
  url = "http://dx.doi.org/10.1002/9780470022184.hmm203"
}

@inbook{sfs,
  author = "D. Suess and J. Fidler and T. Schrefl",
  chapter = "Micromagnetic Simulation of magnetic materials",
  title = "Handbook of Magnetic Materials",
  editor = "K. H. J. Buschow",
  url = "http://www.amazon.com/gp/product/0444518509"
}

@article{fsxzs,
  author = "J. Fernandez-de-Castro and Xiao Shen and Jianhua Xue and Yuming Zhou and S. Sharma",
  title = "Writer Flux Closure and Transition Degradation Mechanism in Perpendicular Recording.",
  journal = "IEEE Trans. Magn. Volume",
  volume = 43,
  pages = "2175-2177",
  url = "http://dx.doi.org/10.1109/TMAG.2007.893122"
}

@article{sb2006,
  author = "W. Scholz and S. Batra",
  title = "Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads",
  journal = "IEEE Trans. Magn.",
  volume = 42,
  year = 2006,
  pages =  "2264--2266",
  url = "http://magnet.atp.tuwien.ac.at/scholz/projects/papers/ieee/scholz_2006_42_2264.pdf"
}

@article{bsr2006,
  author = "S. Batra and W. Scholz and T. Roscamp",
  title = "Effect of thermal fluctuation field on the noise performance of a perpendicular recording system",
  journal = "J. Appl. Phys.",
  volume = 99,
  year = 2006,
  url = "http://magnet.atp.tuwien.ac.at/scholz/projects/papers/jap/batra_2006_99.pdf"
}

@inproceedings{japios2006,
  author = "F. Johnson and S. Amancherla and G.J. Parker and L.E. Iorio and P.R. Subramanian",
  title = "Micromagnetic simulations of the dependence of domain wall width with grain size in systems with cubic and uniaxial anisotropy.",
  booktitle = "Intermag 2006 Conference"
}

@article{kbmb2006,
  author = "A. Kaya and M. Benakli and M.L. Mallary and J.A. Bain",
  title = "A Micromagnetic Study of the Effect of Spatial Variations in Damping in Perpendicular Recording Heads",
  journal = "IEEE Trans. Magn.",
  volume = 42,
  year = 2006,
  pages = "2428--2430",
  url = "http://dx.doi.org/10.1109/TMAG.2006.879430"
}

@article{cclcw2006,
  author = "C. C. Chang and Y. C. Chang and C. M. Lee and C. C. Chen and J. Wu",
  title = "Control of Domain Wall Motion in Permalloy Ring",
  journal = "IEEE Trans. Magn.",
  volume = 42,
  year = 2006,
  pages =  "2960--2962",
  url = "http://dx.doi.org/10.1109/TMAG.2006.878414"
}

@article{bfmfzczg2007,
  author = "Richard P. Boardman and Hans Fangohr and Matthew J. Fairman and J. Zimmermann and Simon J. Cox and Alexander A. Zhukov and Peter A.J. de Groot",
  title = "Micromagnetic modelling of ferromagnetic cones",
  journal = "J. Magn. Magn. Mater.",
  Volume = 312,
  year =  2007,
  Pages = "234-238",
  url ="http://eprints.soton.ac.uk/45900/"
}

@PhdThesis{rb2005,
  author = "Richard Boardman",
  title = "Computer simulation studies of magnetic nanostructures",
  school = "Computational Engineering and Design Group, School of Engineering Sciences, University of Southampton, United Kingdom",
  year = 2005,
  url = "http://www.soton.ac.uk/~rpb/thesis.pdf"
}

@inproceedings{cwwy2006,
  author = "I-Hsin Chung and Robert E. Walkup and Hui-Fang Wen and Hao Yu",
  title = "MPI Performance Analysis Tools on Blue Gene/L",
  booktitle = "ACM/IEEE SC 2006 Conference (SC'06)",
  year = 2006,
  url = "http://sc06.supercomputing.org/schedule/pdf/pap159.pdf"
}

@inproceedings{ch2006,
  author = "I.-H. Chung and J.K. Hollingsworth",
  title = "A Case Study Using Automatic Performance Tuning for Large-Scale Scientific Programs",
  booktitle = "High Performance Distributed Computing, 2006 15th IEEE International Symposium",
  pages = "45--56",
  url = "http://dx.doi.org/10.1109/HPDC.2006.1652135"
}

@article{lkpl2005,
  author = "C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee",
  title = "Multibit MRAM using a pair of memory cells",
  journal = "IEEE Trans. Magn.",
  volume = 41,
  year = 2005,
  pages = "2670-2672",
  url = "http://dx.doi.org/10.1109/TMAG.2005.855288"
}

@article{gscn2005,
  author = "K. Yu. Guslienko and W. Scholz and R. W. Chantrell and V. Novosad",
  title = "Vortex state oscillations in soft magnetic cylindrical dots",
  journal = "Phys. Rev. B",
  volume = 71,
  year = 2005,
  url = "http://dx.doi.org/10.1103/PhysRevB.71.144407"
}

@PhdThesis{mda,
  author = "Massimiliano d'Aquino",
  title = "Nonlinear Magnetization Dynamics in Thin-Films and Nanoparticles",
  school = " Universita di Napoli Federico II.",
  url = "http://www.fedoa.unina.it/148/01/d_Aquino_thesis.pdf"
}

@techreport{ssdfssf2003,
  author = "T. Schrefl and W. Scholz and R. Dittrich and H. Forster and D. Suess and M. Stehno and J. Fidler",
  title = "Micromagnetic Simulations of Domainstructures in Softmagnetic Thin Films",
  url = "http://www.zid.tuwien.ac.at/projekte/2003/03-138-1.html"
}

@inproceedings{sb2006a,
  author = "W. Scholz and S. Batra",
  title = "Effect of write current waveform on magnetization and head field dynamics of perpendicular recording heads",
  booktitle = "Intermag 2006 Conference, San Diego, CA, paper no. EF-03"
}

@article{scholz-batra1,
author = {W. Scholz and S. Batra},
title = "Micromagnetic Simulation of Head Field and Write Bubble Dynamics in Perpendicular Recording",
journal = {IEEE Trans. Magn.},
note = {submitted},
year = 2005
}

@article{scholz-batra2,
author = {W. Scholz and S. Batra},
title = "Micromagnetic Modeling of Head Field Rise Time for High Data-Rate Recording",
journal ={IEEE Trans. Magn.},
volume = 41,
year =2005,
pages = {702-706}
}
@article{daquino-scholz1,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler},
title = "Micromagnetic Analysis of Fast Precessional Switching",
journal ={J. Magn. Magn. Mater.},
volume = {290-291},
year = 2005,
 pages = {510-513}
}
@article{aq-scholz-fid,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and J. Fidler},
title = "Numerical and analytical study of fast precessional switching",
journal ={J. Appl. Phys.},
volume = 95,
year =2004,
 pages = {7055-7057}
}
@inproceedings{gar-tabik-gar,
author = {E. M. Garzon and S. Tabik and I. Garcia and A. R. Bretones},
title = "Multiprocessing of the Time Domain Analysis of Thin-Wire Antennas and Scatterers",
booktitle = {12th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP'04)},
year =2004,
pages = {80--}
}
@inproceedings{aq-scholz-mia,
author = {M. d'Aquino and W. Scholz and T. Schrefl and C. Serpico and G. Miano},
title = "Analysis of fast precessional switching in magnetic thin films",
booktitle = {Proceedings of PIERS (Progress In Electromagnetic Research Symposium)},
year =2004,
pages = {257-260}
}
@article{scholz-fid-seus,
author = {W. Scholz and J. Fidler and T. Schrefl and D. Suess and H. Forster and R. Dittrich and V. Tsiantos},
title = "Numerical Micromagnetic Simulation of Fe-Pt Nanoparticles with Multiple Easy Axes",
journal ={J. Magn. Magn. Mater.},
year = 2004,
 pages = {1524-1525}
}
@article{boardman-zimmerman,
author = {Richard Boardman and Juergen Zimmermann and Hans Fangohr and Alexander Zhukov and Peter de Groot},
title = "Micromagnetic simulation studies of ferromagnetic part-spheres",
journal ={Journal of Applied Physics},
year =2005
}
@article{lim-kim-park,
author = {C. K. Lim and Y. S. Kim and N. Y. Park and J. Lee},
title = "High Density Magnetic Random Access Memory Using a Pair of Asymmetrical Cell",
journal ={IEEE Trans. Magn.},
note = {submitted}
}
@article{scholz-suess2,
author = {W. Scholz and D. Suess and T. Schrefl and and J. Fidler},
title = "Micromagnetic simulation of magnetization reversal in small particles with surface anisotropy",
journal ={J. Appl. Phys.},
volume = 95,
year = 2004,
 pages = {6807-6809}
}
@article{scholz-schrefl1,
author = {W. Scholz and T. Schrefl and J. Fidler and T. Matthias and D. Suess and V. Tsiantos},
title = "Micromagnetic simulation of the pinning and depinning process in permanent magnets",
journal ={IEEE Trans. Magn.},
volume = 39,
year = 2003,
pages = {2920-2922}
}
@article{scholz-guslienko,
author = {W. Scholz and K. Y. Guslienko and V. Novosad and D. Suess and T. Schrefl and R. W. Chantrell and J. Fidler},
title = "Transition from single-domain to vortex state in soft magnetic cylindrical nanodots",
journal ={J. Magn. Magn. Mater.},
volume = 266,
year = 2003,
 pages = {155-163}
}
@article{scholz1,
   author = { W. Scholz and J. Fidler and T. Schrefl and D. Suess and R. Dittrich and H. Forster and V. Tsiantos},
   title  = "Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures",
   journal = "Comp. Mat. Sci",
   year    = 2003,
   pages   = "366--383",
   volume  = 28,
   url     = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/cms03/magpar.pdf}
}
@phdthesis{scholz2,
   author = {W. Scholz},
   title  = "Scalable Parallel Micromagnetic Solvers for Magnetic Nanostructures",
   school = {Vienna University of Technology, Vienna, Austria},
   year   = 2003
}
@article{scholz3,
   author  = {W. Scholz and D. Suess and R. Dittrich and T. Schrefl and V. Tsiantos and H. Forster and J. Fidler},
   title   = "Implementation of a high performance parallel finite element micromagnetics package",
   journal = {J. Magn. Magn. Mater.},
   year    = 2004,
   url     = {http://magnet.atp.tuwien.ac.at/scholz/projects/papers/preprint/scholz/icm2003/scholz_petsc.pdf}
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@InBook{zhanggladwell1,
 AUTHOR=    "W. Zhang and I. Gladwell",
 chapter=     "Performance of MOL for Surface Motion Driven by a Laplacian of Curvature",
 editor=    "Z. Chen and R.E. Ewing and Z.-C. Shi",
 YEAR=      "2000",
 TITLE= "Numerical Treatment of Multiphase Flows in Porous Media, Lecture Notes in Physics, vol. 552",
 publisher="Springer",
 pages =    "4190-"
}
@article{wolf1,
   author = "A. J. Haslan and D. Moldovan and S. R. Phillpot and V. Yamakov",
   title  = "Combined Atomistic and Mesoscale simulation of grain growth in nanocrystalline thin films",
   journal = "Phil. Mag. A",
   year = "2003",
 Lab = {ANL}
}
@article{wolf2,
   author = "A. J. Haslan and D. Moldovan and S. R. Phillpot and H. Gleiter",
   title  = "Mesoscopic simulation of two dimensional grain growth with anisotropic grain-boundary properties",
   journal = "Computational Materials Science",
   year = "2001",
   volume = "23",
   pages = "15--32",
 Lab = {ANL}
}
@article{wolf3,
   author = "D. Moldovan and S. R. Phillpot and A. J. Haslan",
   title  = "Role of grain rotation in grain growth by mesoscale simulation",
   journal = "Phil. Mag. A",
   year = "2002",
   volume = "82",
   pages = "1271--1297",
 Lab = {ANL}
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@article{saut,
   author = { Olivier Saut},
   title  = "Bidimensional Study of the Maxwell-Bloch Model in a Nonlinear Crystal",
   journal = "SIAM Journal on Scientific Computing",
   year    = 2004,
   note    = "submitted",
   url     = {http://mip.ups-tlse.fr/\~{ }saut/data/sisc04.pdf}
}
% LiteralHTML:
% LiteralHTML:  <a name="biology"><H3><center>Biology -- Medical</center></H3>
% LiteralHTML:
@inbook{KhanalLorenziAyachePennec2016,
  title     = {Simulating Patient Specific Multiple Time-Point {MRIs} from a Biophysical Model of Brain Deformation in {Alzheimer's} Disease},
  bookTitle = {Computational Biomechanics for Medicine: Imaging, Modeling and Computing},
  author    = {Bishesh Khanal and Marco Lorenzi and Nicholas Ayache and Xavier Pennec},
  editor    = {Grand R. Joldes and Barry Doyle and Adam Wittek and Poul M.F. Nielsen and Karol Miller},
  pages     = {167--176},
  isbn      = {978-3-319-28329-6},
  doi       = {10.1007/978-3-319-28329-6_15},
  url       = {https://doi.org/10.1007/978-3-319-28329-6_15},
  publisher = {Springer International Publishing},
  year      = {2016},
}
@article{Ataseven,
  author  = {Y. Ataseven and Z. Akaliota n-Acar and C.~E. Acar and N. G. Gen\c{c}er},
  title   = {Parallel implementation of the accelerated BEM approach for EMSI of the human brain},
  journal = {Medical and Biological Engineering and Computing},
  month   = {February},
  year    = {2008},
  note    = {doi 10.1007/s11517-008-0316-0}
}
@article{dennis-eberhart-03,
   author = {B. H. Dennis and R. C. Eberhart and G. S. Dulikravich and S.W. Radons},
   pages = "832-840",
   volume = 125,
   number = 6,
   title  = "Finite-element simulation of cooling of realistic 3-D human head and neck",
   journal = "J Biomech Eng",
   year    = 2003,
   url     = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14986408&dopt=Citation}
}
@conference{gu7174parallel,
  title={{A parallel reduced-space sequential-quadratic programming algorithm for frequency-domain small animal optical tomography}},
  author={Gu, X. and Kim, H.K. and Masciotti, J. and Hielscher, A.H.},
  booktitle={Proc. of SPIE Vol},
  volume={7174},
  number={717406},
  pages={1}
}
@article{barchanski2005using,
  title={{Using domain decomposition techniques for the calculation of low-frequency electric current densities in high-resolution 3D human anatomy models}},
  author={Barchanski, A. and Clemens, M. and De Gersem, H. and Steiner, T. and Weiland, T.},
  journal={COMPEL: The International Journal for Computation and Mathematics in Electrical and Electronic Engineering},
  volume={24},
  number={2},
  pages={458--467},
  issn={0332-1649},
  year={2005},
  publisher={Emerald Group Publishing Limited}
}
@article{MotrescuRienen05,
   author = {V. C. Motrescu and U. van Rienen},
   pages = "227--231",
   volume = 3,
   title  = "Computation of currents induced by ELF electric fields in
             anisotropic human tissues using the Finite Integration Technique",
   journal = "Advances in Radio Science",
   year    = 2005,
   url     = {http://www.copernicus.org/URSI/ars/3/ars-3-227.pdf}
}
@article{MotrescuRienen04,
   author = {V. C. Motrescu and U. van Rienen},
   pages = "309--313",
   volume = 2,
   title  = "Computation of electrostatic fields in anisotropic human tissues using the Finite Integration Technique (FIT)",
   journal = "Advances in Radio Science",
   year    = 2004,
   url     = {http://www.copernicus.org/URSI/ars/ARS_2_1/309.pdf}
}
@InProceedings{dbl2,
  author =       "Enzo A. Dari and Mariano I. Cantero and Raul A. Feijoo",
  title =        "Computational arterial flow modeling using a parallel {Navier-Stokes} solver",
  booktitle =    "ECCOMAS2000",
  year =         "2000",
  url = "http://146.134.8.133/Feijoo/CModComplexos/Conferencias/ECCOMAS2000/Darie/eccomas.html"
}
@Unpublished{cell,
  title = {Parallel Simulation Engines for Whole-Cell Models},
  author = {Markus Schwehm and Nils Gehlenborg and Hendrik Post and Amelie Stein and Kirstin Weber},
  note = {Poster at Second International Conference on Systems Biology (ICSB) 2001},
  url = {http://www.icsb-2001.org/Posters/110_schwehm2.pdf},
  institution = {University of Tubingen, ZBIT - Zentrum fur Bioinformatik Tubingen},
  year = 2001
}
@article{barker2010two,
  title={Two-level Newton and hybrid Schwarz preconditioners for fluid-structure interaction},
  author={Barker, A.T. and Cai, X.C.},
  journal={SIAM Journal on Scientific Computing},
  volume={32},
  number={4},
  pages={2395--2417},
  year={2010},
  publisher={Society for Industrial and Applied Mathematics}
}
@article{barker2010scalable,
  title={Scalable parallel methods for monolithic coupling in fluid-structure interaction with application to blood flow modeling},
  author={Barker, A.T. and Cai, X.C.},
  journal={Journal of Computational Physics},
  volume={229},
  number={3},
  pages={642--659},
  year={2010},
  publisher={Elsevier}
}
@article{barker2009nks,
  title={NKS for fully coupled fluid-structure interaction with application},
  author={Barker, A.T. and Cai, X.C.},
  journal={Domain Decomposition Methods in Science and Engineering XVIII},
  pages={275--282},
  year={2009},
  publisher={Springer}
}
@article{Mirams2013,
  author  = {Chris Luscombe and Geoff Williams and Jordi Munoz-Muriedas and David J Gavaghan and Yi Cui and Gary R Mirams},
  title   = {Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge},
  journal = {Journal of pharmacological and toxicological methods},
  volume  = {68},
  number  = {1},
  pages   = {88--96},
  year    = {2013},
  doi     = {10.1016/j.vascn.2013.04.004}
}

% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img  alt=""
% LiteralHTML: src="images/spine0l.jpg"></center></p>
% LiteralHTML: <center><img  alt=""
% LiteralHTML: src="images/vertebra.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML:Treating fractures of the hip and spine is a major medical cost.
% LiteralHTML:Understanding bone mechanical properties and how they may lead to
% LiteralHTML:fractures is thus an important medical research activity. PETSc and
% LiteralHTML:Prometheus have been used for extremely large scale finite element
% LiteralHTML:simulation of the solid mechanics of a portion of a human spine by a
% LiteralHTML:team of doctors and computational scientists. This computation was
% LiteralHTML:a winner of a Gordon Bell Special Prize at SC2004 and ran scalably
% LiteralHTML:with over 4000 processors.</p>
% LiteralHTML: </font>
@article{arbenz2008scalable,
  title={A scalable multi-level preconditioner for matrix-free $\mu$-finite element analysis of human bone structures},
  author={Arbenz, P. and van Lenthe, G.H. and Mennel, U. and M{\\"u}ller, R. and Sala, M.},
  journal={International Journal for Numerical Methods in Engineering},
  volume={73},
  number={7},
  pages={927--947},
  year={2008},
  publisher={Wiley Online Library}
}
@inproceedings{Adams-04,
	Author = {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and Papadopoulos, P.},
	Booktitle = {ACM/IEEE Proceedings of SC2004: High Performance Networking and Computing},
	Title = {Ultrascalable implicit finite element analyses in solid mechanics with over a half a billion degrees of freedom},
	Note = {Gordon Bell Award},
	Year = {2004}
}
@InProceedings{Adams-03b,
   author =   {Adams, M.~F. and Bayraktar, H.H. and Keaveny, T.M. and  Papadopoulos, P.},
   title =   {Applications of Algebraic Multigrid to Large-Scale Finite Element Analysis of Whole Bone Micro-Mechanics on the IBM SP},
   booktitle = {ACM/IEEE Proceedings of SC2003: High Performance Networking and Computing},
   year = {2003}
}
@inproceedings{oghattas2002,
   author = "Volkan Akcelik and George Biros and Omar Ghattas",
   title  = "Parallel Multiscale {Gauss-Newton-Krylov} Methods For Inverse Wave Propagation",
   booktitle = "Procceedings of SC2002",
   url    ="http://www-2.cs.cmu.edu/\~{ }oghattas/papers/sc2002.pdf",
   note = "Winner of SC2002 Best Paper. A parallel algorithm for inverse problems
           governed by time-dependent PDEs, and scalability results for an inverse
           wave propagation problem of determining the material field of an acoustic
           medium. Using the algorithm, they solved a synthetic inverse wave
           propagation problem though a pelvic bone geometry involving 2.1 million
           inversion parameters in 3 hours on 256 processors.",
   year = "2002"
}
% LiteralHTML:  <a name="biology:cardiology">
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img  alt=""
% LiteralHTML: src="images/heart.jpg">
% LiteralHTML: <img  alt=""
% LiteralHTML: src="images/pump.jpg"></center></p>
% LiteralHTML:
% LiteralHTML:<font color="#FF0000">
% LiteralHTML: Arrhythmias are disorders of the regular rhythmic beating of the
% LiteralHTML: heart; they are the cause of the majority of sudden cardiac
% LiteralHTML: deaths. The heart beat is controlled by electrical signals moving
% LiteralHTML: through the heart. PETSc has been used by several research groups to
% LiteralHTML: simulate the electronic behavior of the heart in an attempt to more
% LiteralHTML: fully understand the developments of arrhthmias.</p>
% LiteralHTML:</font>
@inproceedings{oghattas2000,
   author = "J. Antaki and G. Belloch and O. Ghattas and I. Malcevic
             and G. Miller and N. Walkington",
   title  = "A Parallel Dynamic-Mesh Lagrangian Method for Simulation of Flows with Dynamic
             Interfaces",
   booktitle = "Procceedings of SC2000",
   url    ="http://www.cs.cmu.edu/\~{ }oghattas/papers/sc2000/sc2000.pdf",
   note = "Blood flow modeling at the microscale including effects on individual blood cells,
             for designing heart assist pumps, etc.",
   year = "2000"
}
@InBook{cfps2006,
  author = {P. Colli Franzone and L. F. Pavarino and G. Savare},
  editor = {A. Quarteroni et al.},
  title = {Complex Systems in Biomedicine},
  chapter= {Computational Electrocardiology: mathematical and numerical modeling},
  publisher = {Springer-Verlag},
  pages = {187--241},
  year = {2006}
}
@Inproceedings{cfpst2007,
  author = {P. Colli Franzone and L. F. Pavarino and S. Scacchi and B. Taccardi},
  title = {Determining recovery times from transmembrane action potentials and unipolar electrograms in normal heart tissue},
  booktitle = {FIMH07},
  publisher = {Springer-Verlag},
  volume = {4466},
  pages = {139--149},
  year = {2007}
}
@article{seemann2010framework,
  title={{Framework for Modular, Flexible and Efficient Solving the Cardiac Bidomain Equations Using PETSc}},
  author={Seemann, G. and Sachse, FB and Karl, M. and Weiss, DL and Heuveline, V. and D{\\"o}ssel, O.},
  journal={Progress in Industrial Mathematics at ECMI 2008},
  pages={363--369},
  year={2010},
  publisher={Springer}
}
@INPROCEEDINGS{pft2005,
  AUTHOR  = "Luca F. Pavarino and Piero Colli Franzone and Bruno Taccardi",
  TITLE   = "Monodomain Simulations of Excitation and Recovery in Cardiac Blocks
              with Intramural Heterogeneity",
  BOOKTITLE = "Functional Imaging and modeling of the Heart (FIMH05)",
  PAGES   = "267--277",
  EDITORS = "A. Frangi et al.",
  PUBLISHER = "Springer, Lecture Notes in Computer Science (LNCS), v. 3504",
  YEAR    = "2005"
}
@article{bgcp2005,
   author = "Boyce E. Griffith and Charles S. Peskin",
   title  = "On the order of accuracy of the immersed boundary method: Higher order convergence rates for sufficiently smooth problems",
   journal = "Journal of Computational Physics",
   year = "2005",
   volume = "208",
   pages = "75--105"
}
@article{griffith2007adaptive,
  title={An adaptive, formally second order accurate version of the immersed boundary method},
  author={Griffith, B.E. and Hornung, R.D. and McQueen, D.M. and Peskin, C.S.},
  journal={Journal of Computational Physics},
  volume={223},
  number={1},
  pages={10--49},
  year={2007},
  publisher={Elsevier}
}
@phdthesis{Griffith05,
   author = {Boyce Griffith},
   title  = {Simulating the blood-muscle-valve mechanics of the heart by an adaptive and parallel
             version of the immersed boundary method},
   school = {New York University},
   year   = 2005
}
@phdthesis{Murillo,
   author = {Maria S. Murillo},
   title  = {Parallel Algorithms and Software for Time-Dependent System of Nonlinear Partial Differential Equations
             with an Application in Computational Biology},
   school = {University of Colorado at Boulder},
   year   = 2002
}
@article{spv2004,
   author = "Rodrigo Weber Dos Santos and G. Plank and S. Bauer",
   title  = "Parallel multigrid preconditioner for the cardiac bidomain model",
   journal = "IEEE Trans. Biomed. Eng",
   year = "2004",
   volume = "51",
   pages = "1960--1968"
}
@article{vphl2003,
   author = "E. J. Vigmond and  M. Hughes and G. Plank, L.J. Leon",
   title  = " Computational Tools for Modeling Electrical Activity in Cardiac Tissue",
   journal = "J. Electrocardiol.",
   year = "2003",
   volume = "36",
   pages = "69--74"
}
@INPROCEEDINGS{spbv2003,
        AUTHOR = "Rodrigo Weber Dos Santos and G. Plank and S. Bauer and and E.J. Vigmond",
        TITLE = "Preconditioning Techniques for the Bidomain Equations",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "571--580",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@article{franz-pavir-04,
   author = "P. Colli Franzone and L.~F. Pavarino",
   title  = "A parallel solver for reaction-diffusion systems in computational electrocardiology",
   journal = "Mathematical Models and Methods in Applied Sciences",
   year = "2004",
   volume = "14",
   number = 6,
   pages = "883--912"
}
@article{franz-pavir-05,
   author = "P. Colli Franzone and L.~F. Pavarino and B. Taccardi",
   title  = "Simulating patterns of excitation, repolarization and action potential durationwith cardiac
             Bidomain and Monodomain models",
   journal = "Mathematical Biosciences",
   year = "2005",
   volume = "197",
   number = 1,
   pages = "35--66"
}
@article{franz-pavir-06,
   author = "P. Colli Franzone and L.~F. Pavarino and B. Taccardi",
   title  = "Effects of transmural electrical heterogeneities  and electrotonic interactions on the dispersion of cardiac repolarization
             and action potential duration: a simulation study",
   journal = "Mathematical Biosciences",
   year = "2006",
   volume = "204",
   number = 1,
   pages = "132--165"
}
@INPROCEEDINGS{colli-franz-sim,
        AUTHOR = "P. Colli-Franzone and L.F. Pavarino and B. Taccardi",
        TITLE = "MODELING ANISOTROPIC AND HETEROGENEOUS CARDIAC MODELS: PARALLEL SIMULATIONS",
        BOOKTITLE = "MEDICON and HEALTH TELEMATICS 2004, Health in the Information Society,
                      X Mediterranean Conference on Medical and Biological Engineering",
        URL = "http://cluster.mat.unimi.it/doc/Progetti/Pavarino-LF.pdf",
        YEAR = "2004"
}
@INPROCEEDINGS{pf2003,
        AUTHOR = "Luca F. Pavarino and Piero Colli Franzone",
        TITLE = "Parallel Solution of Cardiac Reaction-Diffusion Models",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "669--776",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@article{maria-is04,
   author = "Maria Murillo and Xiao-Chuan Cai",
   title  = "A fully implicit parallel algorithm for simulating the non-linear electrical activity of the heart",
   journal = "Numerical Linear Algebra with Applications",
   year = "2004",
   volume = "11",
   pages = "261 - 277",
   url = "http://www3.interscience.wiley.com/cgi-bin/abstract/107632540/ABSTRACT"
}
@article{murli2007monitoring,
  title={{Monitoring and Migration of a PETSc-based Parallel Application for Medical Imaging in a Grid computing PSE}},
  author={Murli, A. and Boccia, V. and Carracciuolo, L. and D’Amore, L. and Laccetti, G. and Lapegna, M.},
  journal={Grid-Based Problem Solving Environments},
  pages={421--432},
  year={2007},
  publisher={Springer}
}
@article{Carracciuolo:2006:TPC,
 author = {Carracciuolo, L. and D'Amore, L. and Murli, A.},
 title = {Towards a parallel component for imaging in PETSc programming environment: a case study in 3-D echocardiography},
 journal = {Parallel Comput.},
 volume = {32},
 issue = {1},
 month = {January},
 year = {2006},
 issn = {0167-8191},
 pages = {67--83},
 numpages = {17},
 url = {http://dx.doi.org/10.1016/j.parco.2005.09.001},
 doi = {http://dx.doi.org/10.1016/j.parco.2005.09.001},
 acmid = {1141218},
 publisher = {Elsevier Science Publishers B. V.},
 address = {Amsterdam, The Netherlands, The Netherlands},
 keywords = {Distributed software environment, Image denoising, Non linear PDE, Parallel component},
}
@article{damore2011integration,
  title = {Integration of emerging computer technologies for an efficient image sequences analysis},
  journal = "Integrated Computer-Aided Engineering ",
  volume = "18",
  number = "4",
  pages = "365 - 378",
  year = "2011",
  note = "",
  issn = "1875-8835",
  doi = "http://dx.doi.org/10.3233/ICA-2011-0382",
  url = "http://iospress.metapress.com/content/KM614806M50TKVP7",
  author = "L. D'Amore and D. Casaburi and A. Galletti and L. Marcellino and A. Murli",
  keywords = {Image sequence, pipe and filters, parallel computing, multicore processors},
}
@InProceedings{eth_biwi_00721,
  author = {K. Burckhardt and D. Szczerba and J. Brown and K. Muralidhar and and G. Székely},
  title = {Fast Implicit Simulation of Oscillatory Flow in Human Abdominal Bifurcation using a Schur Complement Preconditioner},
  booktitle = {Euro-Par 2009 Parallel Processing},
  year = {2009},
  month = {August},
  pages = {747-759},
  volume = {5704},
  editor = {H. Sips and D. Epema and and H.-X. Lin},
  series = {Lecture Notes in Computer Science},
  publisher = {Springer},
  keywords = {Aortic aneurysm, flow simulation, streamline diffusion FEM, indefinite matrix, parallel Krylov solver}
}
% LiteralHTML:  <a name="biology:imagingandsurgery">
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img  alt=""
% LiteralHTML: src="images/brain.jpg"></center>
@article{ganser2004deformable,
  title={A deformable digital brain atlas system according to Talairach and Tournoux},
  author={Ganser, K.A. and Dickhaus, H. and Metzner, R. and Wirtz, C.R.},
  journal={Medical Image Analysis},
  volume={8},
  number={1},
  pages={3--22},
  year={2004},
  publisher={Elsevier}
}
@Unpublished{TACCsurgery,
    title  = "TACC supercomputer performs laser cancer surgery on canine",
    url   = "http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser",
    note = {In April, the Lonestar supercomputer at the Texas Advanced Computing Center in Austin performed laser surgery on a dog in
            Houston without the intervention of a surgeon. The treatment was developed collaboratively by computational experts from the Institute
            for Computational Engineering and Sciences (ICES) at UT-Austin, leading technologists from the M.D. Anderson Cancer Center in Houston,
            and cyberinfrastructure specialists and systems from TACC.
            Using precise lasers, state-of-the-art thermal imaging technology, and advanced computational methods, dynamic, data-driven treatments
            are being pursued as a minimally invasive alternative to the standard treatment of cancer.}
}
@article{ffhbresso2008,
   author = "Yusheng Feng and David Fuentes and Andrea Hawkins and Jon Bass and Marissa Nichole Rylander and Andrew Elliott and Anil Shetty and R. Jason Stafford and J. Tinsley Oden",
   title  = "Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment",
   journal = "Engineering with Computers",
   note = "Special issue on Computational Bioengineering",
   year = "2008",
   url = "http://www.tacc.utexas.edu/research/users/features/laser_surgery.pdf"
}
@techreport{dobbhbbbdeffghkkps2008,
 Author      = "K. R. Diller and J. T. Oden and C. Bajaj and J. C. Browne and J. Hazle and I. Babu{\v{s}}ka and J. Bass and
              L. Bidaut and L. Demkowicz and A. Elliott and Y. Feng and D. Fuentes and S. Goswami and A. Hawkins and S. Khoshnevis and B. Kwon and S. Prudhomme and R. J. Stafford",
 TITLE       = "Computational Infrastructure for the Real-Time Patient-Specific Treatment of Cancer",
 year        = 2008,
 INSTITUTION = "University of Texas at Austin",
 URL        = "http://www.tacc.utexas.edu/research/users/features/cancer.pdf"
}
@article{ogdb2004,
   author = "A.A. Oberai and N.H. Gokhale and M.M. Doyley and J.C.Bamber",
   title  = "Evaluation of the Adjoint Equation Based Algorithm for Elasticity Imaging",
   journal = "Physics in Medicine and Biology",
   year = "2004",
   volume = "49",
   pages = "2955--2947"
}
@INPROCEEDINGS{majumdar11,
        AUTHOR = "A. Majumdar and A. Birnbaum and D. Choi and A. Trivedi and S. K. Warfield and K. Baldridge and P. Krysl",
        TITLE = "A Dynamic Data Driven Grid System for Intra-Operative Image Guided Neurosurgery",
        BOOKTITLE = "ICCS 2005",
        PAGES = "672--679",
        editor = "V.S. Sunderam et al.",
        YEAR = "2005"
}
@CONFERENCE{sermesant-etal:03,
  AUTHOR      = {Sermesant, M. and Clatz, O. and Li, Z. and Lanteri, S.
                  and Delingette, H. and Ayache, H.},
  TITLE       = {A parallel implementation of non-rigid registration
                  using a volumetric biomechanical model},
  BOOKTITLE   = {Second International Workshop on Biomedical Image
                  Registration {WBIR'03}},
  ADDRESS     = {Philadelphia, PA, USA},
  PUBLISHER   = {Springer-Verlag},
  EDITOR      = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.},
  SERIES      = {Lecture Notes in Computer Science},
  VOLUME      = {2717},
  PAGES       = {398-407},
  DATE        = {june 23-24},
  YEAR        = {2003},
  url         = {ftp://ftp-sop.inria.fr/epidaure/Publications/Sermesant/WBIR2003Sermesant.pdf}
}
@CONFERENCE{sermesant-etal:04,
  AUTHOR      = {J. Rexilius and S.K. Warfield and C.R.G. Guttmann and X. Wei and R. Benson and L. Wolfson and M. Shenton and
                 H. Handels and R. Kikinis},
  TITLE       = {A Novel Nonrigid Registration Algorithm And Applications},
  BOOKTITLE   = {Medical Image Computing and Computer-Assisted Intervention - MICCAI 2001},
  ADDRESS     = {Philadelphia, PA, USA},
  PUBLISHER   = {Springer-Verlag},
  EDITOR      = {Gee, J.C. and Maintz, J.B.A. and Vannier, M.W.},
  SERIES      = {Lecture Notes in Computer Science},
  VOLUME      = {2208},
  PAGES       = {923},
  YEAR        = {2003},
  url         = {http://www.springerlink.com/app/home/contribution.asp?wasp=6pgwnvthup0amt7g9j4k&referrer=parent&backto=issue,105,251;journal,1191,1949;linkingpublicationresults,1:105633,1}
}
@article{warfield-haker-talos-05,
   author = "Simon K. Warfield and Steven J. Haker and Ion-Florin Talos and Corey A. Kemper and
             Neil Weisenfeld and Andrea U.J. Mewes and Daniel Goldberg-Zimring and Kelly H. Zou and
             Carl-Fredrik Westin and William M. Wells and Clare M.C. Tempany and Alexandra Golby and
             Peter M. Black and Ferenc A. Jolesz and Ron Kikinis",
   title  = "Capturing intraoperative deformations: research experience at Brigham and Women's hospital",
   journal = "Medical Image Analysis",
   url    ="http://splweb.bwh.harvard.edu:8000/pages/papers/warfield/capturing-intraoperative-deformations-MIA2005.pdf",
   year   = "2005"
}
@article{brain3,
   author = "Simon K. Warfield and Florin Talos and Alida Tei and Arya Nabavi and Matthieu Ferrant and Peter McL. Black and
             Ferenc A. Jolesz and Ron Kikinis",
   title  = "Real-Time Registration of Volumetic Brain {MRI} by Biomechanical Simulation of Deformation during Image Guided
             Neurosurgery",
   journal = "Computing and Visualization in Science",
   url     ="http://splweb.bwh.harvard.edu:8000/pages/ppl/warfield/papers/2002/warfield-2002-cvs-appeared.pdf",
   year    = "2002"
}
@article{brain2,
   author = "Matthieu Ferrant and Arya Nabavi and Benoit Macq and
             Ferenc A. Jolesz and Ron Kikinis and Simon K. Warfield",
   title  = "Registration of {3D} Intraoperative {MR} Images of the Brain using a Finite Element Biomechanical Model",
   journal = "IEEE Transactions on Medical Imaging",
   url    ="http://splweb.bwh.harvard.edu:8000/pages/papers/ferrant/tmi2001.pdf",
   year   = "2001"
}
@inproceedings{brain1,
   author = "Simon K. Warfield and Matthieu Ferrant and Xavier Gallez and Arya Nabavi and
             Ferenc A. Jolesz and Ron Kikinis",
   title  = "Real-Time Biomechanical Simulation of Volumetric Brain Deformation for Image Guided Neurosurgery",
   booktitle = "Proceedings of SC2000",
   url    ="http://www.sc2000.org/techpapr/papers/pap.pap230.pdf",
   year = 2000
}
@article{Vanne06,
   author  = "V. Kolehmainen and A. Vanne and S. Siltanen and S. Jarvenpaa and J.P. Kaipio and M. Lassas and M. Kalke",
   title   = "Parallelized Bayesian inversion for three-dimensional dental X-ray imaging",
   journal = "IEEE Transactions on Medical Imaging",
   volume = "25",
   number = "2",
   month = "February",
   year = "2006",
   pages = "218--228"
}
@inproceedings{KnepleyBardhan2015,
   title     = {Work/Precision Tradeoffs in Continuum Models of Biomolecular Electrostatics},
   author    = {Matthew G. Knepley and Jaydeep P. Bardhan},
   booktitle = {Proceedings of ASME 2015 International Mechanical Engineering Congress \& Exposition},
   volume    = {9},
   pages     = {V009T12A04},
   doi       = {10.1115/IMECE2015-53579},
   year      = {2015},
}
@inproceedings{BardhanKnepley2015,
  title     = {Multiscale models and approximation algorithms for protein electrostatics},
  author    = {Jaydeep P. Bardhan and Matthew G. Knepley},
  booktitle = {Boundary Elements and Other Mesh Reduction Methods XXXVIII},
  volume    = {61},
  pages     = {163--174},
  url       = {http://www.witpress.com/Secure/elibrary/papers/BEM38/BEM38013FU1.pdf},
  doi       = {10.2495/BEM380131},
  publisher = {WIT Press},
  year      = {2015},
}
% LiteralHTML:
% LiteralHTML:  <a name="fusion"><H3><center>Fusion</center></H3>
% LiteralHTML:
@article{AdamsHirvijokiKnepleyBrownIsaacMills2017,
  title    = {{Landau} Collision Integral Solver with Adaptive Mesh Refinement on Emerging Architectures},
  author   = {Mark F. Adams and Eero Hirvijoki and Matthew G. Knepley and Jed Brown and Tobin Isaac and Richard Mills},
  journal = {SIAM Journal on Scientific Computing},
  volume   = {39},
  number   = {6},
  pages    = {C452--C465},
  url      = {http://epubs.siam.org/doi/abs/10.1137/17M1118828},
  eprint   = {1702.08880},
  doi      = {10.1137/17M1118828},
  year     = {2017}
}

@article{Hirvijoki2017,
author = {E. Hirvijoki and M. F. Adams},
title = {Conservative discretization of the {Landau} collision integral},
journal = {Physics of Plasmas},
volume = {24},
number = {3},
pages = {032121},
year = {2017},
doi = {10.1063/1.4979122},
URL = { http://dx.doi.org/10.1063/1.4979122},
eprint = { http://dx.doi.org/10.1063/1.4979122}
}

@article{lsmh2014,
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@article{lpcep2014,
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@article{facets-scidac08,
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@article{facets-scidac09,
   title   = "Concurrent, Parallel, Multiphysics Coupling in the {FACETS} Project",
   author  = "J. Cary and J. Candy and J. Cobb and R. H. Cohen and T. Epperly and
              D. Estep and S. Krasheninnikov and A. Malony and D. McCune and
              L. McInnes and A. Pankin and S. Balay and J. Carlsson and M. R. Fahey and
              R. Groebner and A. Hakim and S. Kruger and M. Miah and A. Pletzer and
              S. Shasharina and S. Vadlamani and D. Wade-Stein and T. Rognlien and
              A. Morris and S. Shende and G. W. Hammett and K. Indireshkumar and
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@inProceedings{facets-scidac10,
   title   = "Coupled Whole Device Simulations of Plasma Transport in Tokamaks with the {FACETS} Code",
   author  = "A. Hakim and J. Cary and J. Candy and J. Cobb and R. Cohen and T. Epperly and D. Estep
              and S. Krasheninnikov and A. Malony and D McCune and L.C. McInnes and A. Pankin and S. Balay
              J. Carlsson and M. Fahey and R. Groebner and S. Kruger and M. Miah and A. Pletzer and
              S. Shasharina and S. Vadlamani and D. Wade-Stein and T. Rognlein and A. Morris and
              S. Shende and G. Hammett and K. Indareshkumar and A. Pigarov and H. Zhang",
   booktitle = "Proceedings of SciDAC 2010 Conference",
   year    = 2010,
   url = "http://computing.ornl.gov/workshops/scidac2010/papers/fusion_a_hakim.pdf"
}
@inproceedings{facets-fec2010,
   title     = "Concurrent, Parallel, Coupled Core-Edge Simulations of Pedestal Formation Using the {FACETS} Framework",
   author    = "J. Cary and A. Hakim and A. Pletzer and M. Miah and S. Kruger and S. Shasharina
                and S. Vadlamani and J. Carlsson and A. Pankin and T. Rognlien and R. Cohen and
                D. McCune and K. Indireshkumar and A. Pigarov and L.C. McInnes and H. Zhang",
   booktitle = "Proceedings of the 23rd annual IAEA Fusion Energy Conference (FEC 2010), Daejon, Republic of Korea",
   year      = 2010
}
@inproceedings{facets-epdp2010,
   title     = "{FACETS}: A Framework for Parallel Coupling of Fusion Components",
   author    = "J. Cary and A. Hakim and M. Miah and S. Kruger and A. Pletzer and S. Shasharina and S. Vadlamani
                and A. Pankin and R. Cohen and T. Epperly and T. Rognlien and R. Groebner and S. Balay and
                L. McInnes and H. Zhang",
   booktitle = "Proceedings of Euromicro PDP 2010 (The 18th Euromicro International Conference on Parallel,
                Distributed and Network-Based Computing), Pisa, Italy",
   year      = 2010
}
@article{CarlssonCary09,
  author  = {Johan Carlsson, John R. Cary},
  title   = {The hypersecant Jacobian approximation for quasi-Newton solves of sparse nonlinear systems},
  journal = {arXiv},
  year    = {2009},
  note    = {http://arxiv.org/abs/0905.1054},
  url     = {http://arxiv.org/pdf/0905.1054v1}
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@InProceedings{oshahjs2006,
  author =       {F. Ogando and A. Signell and J.A. Heikkinen and M. Aspn\"as and S. Henriksson and S.J. Janhunen and T.P. Kiviniemi},
  title =        "Performance enhancements to ELMFIRE gyrokinetic code leading to new ranges of application",
  booktitle =    "33rd EPS Conference on Plasma Phys.",
  year =         "2006",
  url = "http://epsppd.epfl.ch/Roma/pdf/P4_153.pdf",
  note = "European fusion code"
}
@article{Zhu2006,
  author = "P. Zhu and A. Bhattacharjee and K. Germaschewski",
  title = "Intermediate nonlinear evolution of the Parker instability: Formation of convection-induced discontinuities and absence of finite-time singularities",
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@InProceedings{ppc2005,
  author =       "B. Philip and M. Pernice and L.Chacon",
  title =        "Solution of Reduced Resistive Magnetohydrodynamics using Implicit Adaptive Mesh Refinement",
  booktitle =    "Proceedings of the 16th International Conference on  Domain Decomposition methods",
  year =         "2005",
  Lab = {LANL}
}
@article{PP2005,
  author  =       "M. Pernice and B. Philip",
  title   =        "Solution of Equilibrium Radiation Diffusion Problems using Adaptive Mesh Refinement",
  year    =         "2005",
  journal = "SIAM J. of Sci. Comput.",
  Lab     = {LANL}
}
@article{GT2004,
  author =       "A. H. Glasser and X. Z. Tang",
  title =        "The SEL macroscopic modeling code",
  year =         "2004",
  journal = "Computer Physics Communications",
  pages = "237--243",
  volume = "164",
 Lab = {LANL}
}
@article{NL2006,
  author =       "Y. Nishimura and Z.Lin",
  title =        "A finite element  mesh in a tokamak edge geometry",
  year =         "2006",
  journal = "Contributions to Plasma Physics",
  volume = 22,
  Lab = {PPPL}
}
@article{NLLE2004,
  author =       "Y. Nishimura and Z.Lin and J.Lewandowski and S.Ethier",
  title =        "A finite element Poisson solver for gyrokinetic particle simulations in a global field aligned mesh",
  year =         "2006",
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  volume = 214,
  pages = "657",
  Lab = {PPPL}
}
@InProceedings{lnlle2004,
  author =       "J.L.V Lewandowski and Y.Nishimura and W.W.Lee and Z.Lin and S. Ethier",
  title =        "Global gyrokinetic Particle-in-cell Simulations with Trapped Electrons",
  booktitle =    "Sherwood Fusion Theory Conference, Missoula, MT",
  year =         "2004",
  url = "http://www.sherwoodtheory.org/sherwood04/program/1e15.pdf",
  Lab = {PPPL}
}
@InProceedings{NLCLEW2004,
  author =       "Y. Nishimura and Z.Lin and L.Chen and J.Lewandowski and S.Ethier and W. Wang",
  title =        "Electromagnetic gyrokinetic simulation with a fluid-kinetic hybrid electron model",
  booktitle =    "Sherwood Fusion Theory Conference, Missoula, MT",
  year =         "2004",
  url = "http://www.sherwoodtheory.org/sherwood04/program/1C32.pdf",
  Lab = {PPPL}
}
@Article{tb1,
   author = "X.~Z.~Tang and A.~H.~Boozer",
   title = "Numerical studies of a steady state axisymmetric co-axial helicity injection plasma",
   journal="Physics of Plasmas",
   year="2004",
   pages="171--185",
   volume="11",
 Lab = {LANL}
}
@Unpublished{nlcw,
  title = {Inclusion of electromagnetic effects into gyrokinetic particle simulations},
  author = {Y. Nishimura and Z.Lin and L.Chen and W. Wang},
  note = {American Physical Society 45th Annual Meeting Division of Plasma Physics, Albuquerque, New Mexico, October 2003},
  year = "2003"
}
@techreport{tang2001,
 Author      = "X. Z. Tang and G. Y. Fu and S. C. Jardin and L. L. Lowe and W. Park and H. R. Strauss",
 TITLE       = "Resistive Magnetohydrodynamics Simulation of Fusion Plasmas",
 year        = 2001,
 INSTITUTION = "Princeton Plasma Physics Laboratory",
 number     = "PPPL-3532",
 URL        = "http://www.pppl.gov/pub_report/2001/PPPL-3532.pdf",
 note       = "Presented at 10th Society for Industrial and Applied Mathematics (SIAM) Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 12-14, 2001.",
 Lab = {PPPL}
}
% LiteralHTML:
% LiteralHTML:  <a name="geosciences"><H3><center>Geosciences</center></H3>
% LiteralHTML:
@article{ValeraThomasGarciaCastillo2019,
  author  = {Manuel Valera and Mary P. Thomas and Mariangel Garcia and Jose E. Castillo},
  title   = {Parallel Implementation of a {PETSc-Based} Framework for the General Curvilinear Coastal Ocean Model},
  journal = {Journal of Marine Science and Engineering},
  volume  = {7},
  number  = {6},
  article-number = {185},
  url     = {https://www.mdpi.com/2077-1312/7/6/185},
  issn    = {2077-1312},
  doi     = {10.3390/jmse7060185},
  year    = {2019},
}
@article{FuruichiMat2015,
  title={Implicit solution of the material transport in Stokes flow simulation: Toward thermal convection simulation surrounded by free surface},
  author={Mikito Furuichi and Dave A May},
  journal={Computer Physics Communications},
  volume={192},
  pages={1--11},
  year={2015},
}
@article{SharplesMoresiVelicJadamecMay2016,
  title   = {Simulating faults and plate boundaries with a transversely isotropic plasticity model},
  author  = {Wendy Sharples and Louis N Moresi and Mirko Velic and Margarete A Jadamec and Dave A May},
  journal = {Physics of the Earth and Planetary Interiors},
  volume  = {252},
  pages   = {77--90},
  year    = {2016}
}
@article{SpiegelmanMayWilson2016,
  title={On the solvability of incompressible Stokes with viscoplastic rheologies in geodynamics},
  author={Marc Spiegelman and Dave A May and Cian R Wilson},
  journal={Geochemistry, Geophysics, Geosystems},
  volume={17},
  number={6},
  pages={2213--2238},
  year={2016},
}
@article{BuiterEtAl2016,
  title={Benchmarking numerical models of brittle thrust wedges},
  author={Susanne JH Buiter and Guido Schreurs and Markus Albertz and Taras V Gerya and Boris Kaus and Walter Landry and
                  Laetitia {Le Pourhiet} and Yury Mishin and David L Egholm and Michele Cooke and Bertrand Maillot and
                  Cedric Thieulot and Tony Crook and Dave May and Pauline Souloumiac and Christopher Beaumont},
  journal={Journal of structural geology},
  volume={92},
  pages={140--177},
  year={2016},
}
@article{AfanasievBoehmDrielKrischerRietmannMayKnepleyFichtner2019,
  title   = {Modular and flexible spectral-element waveform modelling in two and three dimensions},
  author  = {Michael Afanasiev and Christian Boehm and Martin van Driel and Lion Krischer and Max Rietmann and Dave A. May and Matthew G. Knepley and Andreas Fichtner},
  journal = {Geophysical Journal International},
  volume  = {216},
  number  = {3},
  pages   = {1675--1692},
  doi     = {10.1093/gji/ggy469},
  year    = {2019}
}
@article {YoungOppenheimDimant2017,
  author  = {Matthew A. Young and Meers M. Oppenheim and Yakov S. Dimant},
  title   = {Hybrid simulations of coupled Farley-Buneman/gradient drift instabilities in the equatorial E region ionosphere},
  journal = {Journal of Geophysical Research: Space Physics},
  volume  = {122},
  number  = {5},
  issn    = {2169-9402},
  url     = {http://dx.doi.org/10.1002/2017JA024161},
  doi     = {10.1002/2017JA024161},
  pages   = {5768--5781},
  year    = {2017},
}
@article{RioussetPatyLillisFillingimEnglandWithersHale2013,
  title   = {Three-dimensional multifluid modeling of atmospheric electrodynamics in Mars' dynamo region},
  author  = {Jeremy A Riousset and Carol S Paty and Robert J Lillis and Matthew O Fillingim and Scott L England and Paul G Withers and John P M Hale},
  journal = {Journal of Geophysical Research: Space Physics},
  volume  = {118},
  number  = {6},
  pages   = {3647--3659},
  year    = {2013},
  publisher = {Wiley Online Library}
}
@article{chien2016representation,
  title={Representation of topography by partial steps using the immersed boundary method in a vector vorticity equation model (VVM)},
  author={Chien, Mu-Hua and Wu, Chien-Ming},
  journal={Journal of Advances in Modeling Earth Systems},
  year={2016},
  publisher={Wiley Online Library}
}
@article{berger2015parallel,
  title={Parallel preconditioners for monolithic solution of shear bands},
  author={Berger-Vergiat, Luc and McAuliffe, Colin and Waisman, Haim},
  journal={Journal of Computational Physics},
  year={2015},
  publisher={Elsevier}
}
@article{May2015496,
title = "A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous {S}tokes flow ",
journal = "Computer Methods in Applied Mechanics and Engineering ",
volume = "290",
number = "0",
pages = "496--523",
year = "2015",
issn = "0045-7825",
doi = "http://dx.doi.org/10.1016/j.cma.2015.03.014",
url = "http://www.sciencedirect.com/science/article/pii/S0045782515001243",
author = "D.A. May and J. Brown and L. {Le Pourhiet}",
}
@article{IsaacKnepley2017,
  title   = {Support for Non-conformal Meshes in {PETSc}'s {DMPlex} Interface},
  author  = {Tobin Isaac and Matthew G. Knepley},
  journal = {ACM Transaction on Mathematical Software},
  eprint  = {1508.02470},
  note    = {In review},
  year    = {2017}
}
@article{KnepleyLangeGorman2017,
  title     = {Unstructured Overlapping Mesh Distribution in Parallel},
  author    = {Matthew G. Knepley and Michael Lange and Gerard J. Gorman},
  journal   = {ACM Transactions on Mathematical Software},
  eprint    = {1506.06194},
  note      = {submitted},
  year      = {2017}
}
@article{LangeMitchellKnepleyGorman2015,
  title     = {Efficient mesh management in {Firedrake} using {PETSc-DMPlex}},
  author    = {Michael Lange and Lawrence Mitchell and Matthew G. Knepley and Gerard J. Gorman},
  journal   = {SIAM Journal on Scientific Computing},
  volume    = {38},
  number    = {5},
  pages     = {S143--S155},
  eprint    = {http://arxiv.org/abs/1506.07749},
  url       = {http://epubs.siam.org/doi/abs/10.1137/15M1026092},
  year      = {2016}
}
@inproceedings{LangeKnepleyGorman2015,
  title     = {Flexible, Scalable Mesh and Data Management using {PETSc DMPlex}},
  author    = {Michael Lange and Matthew G. Knepley and Gerard J. Gorman},
  booktitle = {Proceedings of the Exascale Applications and Software Conference},
  month     = {April},
  url       = {http://www.easc2015.ed.ac.uk/sites/default/files/attachments/EASC15Proceedings.pdf},
  year      = {2015}
}
@article{RathgeberHamMitchellLangeLuporiniMcRaeBerceaMarkallKelly2016,
  title   = {Firedrake: automating the finite element method by composing abstractions},
  author  = {Florian Rathgeber and David A Ham and Lawrence Mitchell and Michael Lange and Fabio Luporini and Andrew TT McRae and Gheorghe-Teodor Bercea and Graham R Markall and Paul HJ Kelly},
  journal = {ACM Transactions on Mathematical Software (TOMS)},
  volume  = {43},
  number  = {3},
  pages   = {24},
  year    = {2016},
}
@article{MitchellMuller2016,
  title   = {High level implementation of geometric multigrid solvers for finite element problems: Applications in atmospheric modelling},
  author  = {Lawrence Mitchell and Eike Hermann M{\"u}ller},
  journal = {Journal of Computational Physics},
  volume  = {327},
  pages   = {1--18},
  year    = {2016},
}
@article{McRaeBerceaMitchellHamCotter2016,
  title   = {Automated generation and symbolic manipulation of tensor product finite elements},
  author  = {Andrew TT McRae and Gheorghe-Teodor Bercea and Lawrence Mitchell and David A Ham and Colin J Cotter},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {38},
  number  = {5},
  pages   = {S25--S47},
  year    = {2016},
}
@article{BerceaMcRaeHamMitchellRathgeberNardiLuporiniKelly2016,
  title    = {A structure-exploiting numbering algorithm for finite elements on extruded meshes, and its performance evaluation in {Firedrake}},
  author   = {Gheorghe-Teodor Bercea and Andrew TT McRae and David A Ham and Lawrence Mitchell and Florian Rathgeber and L. Nardi and Fabio Luporini and Paul HJ Kelly},
  journal  = {Geoscientific Model Development},
  volume   = {9},
  number   = {10},
  pages    = {3803--3815},
  url      = {https://www.geosci-model-dev.net/9/3803/2016/},
  doi      = {10.5194/gmd-9-3803-2016},
  year     = {2016},
}
@inproceedings{MarkallRathgeberMitchellLoriantBertolliHamKelly2013,
  author    = {Graham R. Markall and Florian Rathgeber and Lawrence Mitchell and Nicolas Loriant and Carlo Bertolli and David A. Ham and Paul HJ Kelly},
  editor    = {Julian Martin Kunkel and Thomas Ludwig and Hans Werner Meuer},
  title     = {Performance-Portable Finite Element Assembly Using {PyOP2} and {FEniCS}},
  booktitle = {Proceedings of 28th International Supercomputing Conference, ISC 2013},
  publisher = {Springer Berlin Heidelberg},
  pages     = {279--289},
  isbn      = {978-3-642-38750-0},
  doi       = {10.1007/978-3-642-38750-0_21},
  url       = {http://dx.doi.org/10.1007/978-3-642-38750-0_21},
  year      = {2013},
}
@article{KirbyMitchell2017,
  title   = {Solver composition across the {PDE}/linear algebra barrier},
  author  = {Robert C Kirby and Lawrence Mitchell},
  journal = {arXiv preprint arXiv:1706.01346},
  year    = {2017}
}

@article{saibaba2012application,
  title   = {Application of hierarchical matrices to linear inverse problems in geostatistics},
  author  = {Saibaba, Arvind Krishna and Ambikasaran, Sivaram and Yue Li, J and Kitanidis, Peter K and Darve, Eric F},
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  number  = {5},
  pages   = {857},
  year    = {2012}
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@article{CollignonKausMayFernandez14,
Author = {Collignon, M. and Kaus, B. and May, D.A. and Fern\'andez, N.},
title = {Influences of surface processes on fold growth during {3-D} detachment folding},
Journal = {Geochem Geophy Geosy},
year = 2014
}
@article{FernandezKaus14,
Author = {Fern\'andez, N. and Kaus, B.},
title = {Fold interaction and wavelength selection in 3D models of multilayer detachment folding},
Journal = {Tectonophysics},
year = 2014
}
@article{BaumannKausPopov14,
Author = {Baumann, T. and Kaus, B. J. P. and Popov, A.},
title =  {Constraining effective rheology through parallel joint geodynamic inversion},
Journal = {Tectonophysics},
year = 2014
}
@article{LechmannSchmalholzHetenyiMayKaus14,
Author = {Lechmann,  S. M. and Schmalholz, S. M. and Hetenyi, G. and May, D. A. and Kaus, B. J. P.},
title =  {Quantifying the impact of mechanical layering and underthrusting on the dynamics of the modern
          {India-Asia} collisional system with {3-D} numerical models},
Journal = { Journal of Geophysical Research - Solid Earth},
year = 2014
}
@inbook{FernandezKaus14b,
Author = {Fern\'andez N. and Kaus B.J.P.},
title = {Analytical and numerical investigation of 3D multilayer detachment},
booktitle = {Mathematics of Planet Earth},
editor = {Pardo-Ig\'uzquiza E. and Guardiola-Albert C. and Heredia J. and Moreno-Merino L. and Dur\'an J.J. and Vargas-Guzman J.A.},
publisher = {Springer},
year = 2014
}
@article{Hossein-Hsueh-EtAl-2014a,
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@unpublished{Leon-Baldelli-Bourdin-2014a,
        Author = {Le\'{o}n Baldelli, A.A. and Bourdin, B.},
        Month = {08},
        Note = {Submitted.},
        Title = {On the asymptotic derivation of Winkler-type energies from {3D} elasticity},
        Year = {2014}
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@article{Leon-Baldelli-Babadjian-EtAl-2013a,
        Author = {Leòn-Baldelli, A. A. and Babadjian, J.-F. and Bourdin, B. and Henao, D. and Maurini, C.},
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@inproceedings{Bourdin-Chukwudozie-EtAl-2013a,
        Author = {Bourdin, B. and Chukwudozie, C. and Yoshioka, K.},
        Booktitle = {Proceedings of the 38th Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, CA},
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@article{Maurini-Bourdin-EtAl-2012a,
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@inproceedings{Bourdin-Chukwudozie-EtAl-2012a,
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@article{MillerDawsonFarthingHouHuangKeesKelleyLangtangen13,
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  url     = {http://www.sciencedirect.com/science/article/pii/S0309170812001431}
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@article{ScheltingaMyersPietrzak10,
  author={Terwisscha van Scheltinga, ArjenD. and Myers, PaulG. and Pietrzak, JulieD.},
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  year={2010},
  issn={1616-7341},
  doi={10.1007/s10236-010-0356-5},
  url={http://dx.doi.org/10.1007/s10236-010-0356-5},
  publisher={Springer-Verlag},
  keywords={Ocean modelling; Unstructured meshes; Sea ice; Arctic Ocean; Canadian Arctic Archipelago; Freshwater flux},
  language={English}
}
@inbook{DeStefanoAndreasiSecchi13,
  author    = {M. De Stefano and F. Golfré Andreasi and A. Secchi},
  title     = {Towards preconditioned nonlinear conjugate gradients for generic geophysical inversions},
  booktitle = {SEG Technical Program Expanded Abstracts 2013},
  chapter   = {626},
  pages     = {3226--3230},
  doi       = {10.1190/segam2013-0244.1},
  URL       = {http://library.seg.org/doi/abs/10.1190/segam2013-0244.1},
  eprint    = {http://library.seg.org/doi/pdf/10.1190/segam2013-0244.1}
}
@article{PourhietHuetMayLabrousseJolivet12,
  author  = {L. {Le Pourhiet} and B. Huet and D. A. May and L. Labrousse and L. Jolivet},
  title   = {Kinematic interpretation of the 3D shapes of metamorphic core complexes},
  journal = {Geochem. Geophys. Geosyst.},
  volume  = {13},
  pages   = {Q09002},
  year    = {2012},
  doi     = {doi:10.1029/2012GC004271}
}
@article{LechmannMayKausSchmalholz11,
  author  = {S. M. Lechmann and D. A. May and B. J. P. Kaus and S. M. Schmalholz},
  title   = {Comparing thin-sheet models with {3-D} multilayer models for continental collision},
  journal = {Geophysical Journal International},
  volume  = {187},
  pages   = {10--33},
  year    = {2011},
  doi     = {doi: 10.1111/j.1365-246X.2011.05164.x}
}
@article{stefano:R69,
author = {Michele De Stefano and Federico Golfr\'{e} Andreasi and Simone Re and Massimo Virgilio and Fred F. Snyder},
collaboration = {},
title = {Multiple-domain, simultaneous joint inversion of geophysical data with application to subsalt imaging},
publisher = {SEG},
year = {2011},
journal = {Geophysics},
volume = {76},
number = {3},
pages = {R69-R80},
keywords = {geophysical image processing; inverse problems; seismology},
url = {http://dx.doi.org/10.1190/1.3554652},
doi = {10.1190/1.3554652}
}
@article{stefano:806,
author = {Michele De Stefano},
collaboration = {},
title = {Simultaneous joint inversion for susceptibility and velocity},
publisher = {SEG},
year = {2011},
journal = {SEG Technical Program Expanded Abstracts},
volume = {30},
number = {1},
pages = {806-810},
keywords = {3D; imaging; inversion; magnetics; multiparameter},
url = {http://dx.doi.org/10.1190/1.3628198},
doi = {10.1190/1.3628198}
}
@article{MayKnepley2011,
  author  = {Dave A. May and Matthew G. Knepley},
  title   = {Optimal, scalable forward models for computing gravity anomalies},
  journal = {Geophysical Journal International},
  volume  = {187},
  number  = {1},
  pages   = {161--177},
  url     = {http://arxiv.org/abs/1107.5951},
  note    = {\url{http://arxiv.org/abs/1107.5951}},
  year    = {2011}
}
@inproceedings{BourdinKnepleyMaurini2010,
  author    = {Blaise Bourdin and Matthew G. Knepley and C. Maurini},
  title     = {Numerical Simulation of Reservoir Stimulation - A Variational Approach},
  booktitle = {Proceedings of the 37th Stanford Geothermal Workshop},
  url       = {http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf},
  note      = {\url{http://www.geothermal-energy.org/pdf/IGAstandard/SGW/2011/bourdin.pdf}},
  address   = {Stanford, CA},
  year      = {2010}
}
@inproceedings{BourdinKnepleyMaurini2010b,
  author    = {Blaise Bourdin and Matthew G. Knepley and C. Maurini},
  title     = {Secondary Thermal Cracks in {EGS}: a Variational Approach},
  booktitle = {Proceedings of the 34th Annual Meeting of the Geothermal Resources Council},
  url       = {https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf},
  note      = {\url{https://www.math.lsu.edu/~bourdin/Biography_assets/Bourdin-Knepley-Maurini-2010.pdf}},
  address   = {Sacramento, CA},
  year      = {2010}
}
@article{chen2007full,
  title={Full 3D tomography for the crustal structure of the Los Angeles region},
  author={Chen, P. and Zhao, L. and Jordan, T.H.},
  journal={Bulletin of the Seismological Society of America},
  volume={97},
  number={4},
  pages={1094},
  year={2007},
  publisher={Seismol Soc America}
}
@article {brown2010ens,
  author = {Brown, Jed},
  affiliation = {Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie (VAW), ETH Zürich, Zürich, Switzerland},
  title = {Efficient Nonlinear Solvers for Nodal High-Order Finite Elements in {3D}},
  journal = {Journal of Scientific Computing},
  publisher = {Springer Netherlands},
  issn = {0885-7474},
  keyword = {Mathematics and Statistics},
  pages = {48-63},
  volume = {45},
  issue = {1},
  url = {http://dx.doi.org/10.1007/s10915-010-9396-8},
  doi = {10.1007/s10915-010-9396-8},
  year = {2010}
}
@phdthesis{brown2011,
  title = {Computational methods for ice flow simulation},
  author = {Jed Brown},
  school = {ETH Z{\"u}rich},
  year = 2011
}
@article{brown2013tmeice,
  title={Achieving textbook multigrid efficiency for hydrostatic ice flow},
  author={Jed Brown and Barry F. Smith and Aron Ahmadia},
  journal={SIAM Journal on Scientific Computing},
  volume=35,
  number=2,
  year={2013},
  pages={359--375},
  doi={10.1137/110834512},
  note={Also preprint ANL/MCS-P743-1298}
}
@inproceedings{brown2013quasinewton,
  author    = {Jed Brown and Peter Brune},
  title     = {Low-rank quasi-{N}ewton updates for robust {J}acobian lagging in {N}ewton-type methods},
  year      = {2013},
  booktitle = {International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering},
  pages     = {2554--2565},
}
@misc{spiegelman-siampp10,
   title = "Block Preconditioners and Advanced Software for Multiphysics Problems in Solid Earth Geodynamics",
   author = "Marc Spiegelman",
   note = "presentation at the 2010 SIAM Conference on Parallel Processing for Scientific Computing",
   year = 2010
}
@Article{	  Schauer2011a,
 author	= "Marco Schauer and Sabine Langer and Jose E. Roman and Enrique S. Quintana-Ort\'{\i}",
 title		= "Large scale simulation of wave propagation in soils interacting with structures using {FEM} and {SBFEM}",
 journal	= "Journal of Computational Acoustics",
 volume	= "19",
 number	= "1",
 pages		= "75--93",
 year		= "2011",
 doi           = "http://dx.doi.org/10.1142/S0218396X11004316"
}
@misc{bsa2010,
 author =     {J. Brown and B. Smith and A. Ahmadia},
 title =      {Achieving textbook multigrid efficiency for hydrostatic ice sheet flow},
 note =    {submitted to SIAM Journal on Scientific Computing},
 year =       {2012},
}

@article{KellerKatz2016,
  title   = {The Role of Volatiles in Reactive Melt Transport in the Asthenosphere},
  author  = {Tobias Keller and Richard F. Katz},
  journal = {Journal of Petrology},
  doi     = {10.1093/petrology/egw030},
  URL     = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.abstract},
  eprint  = {http://petrology.oxfordjournals.org/content/early/2016/07/15/petrology.egw030.full.pdf+html},
  year    = {2016},
}

@Article{weatherley12,
  author =	 {S. Weatherley and R.F. Katz},
  title =	  {Melting and channelized magmatic flow in chemically
                 heterogeneous, upwelling mantle},
  journal =	  {Geochem.\ Geophys.\ Geosys.},
  year =   2012,
  volume =  13,
  number =   1,
  pages =        {Q0AC18},
  doi =		  {10.1029/2011GC003989},
}

@Article{katz12,
  author =       {R.F. Katz and S. Weatherley},
  title =        {Consequences of mantle heterogeneity for melt extraction
                  at mid-ocean ridges},
  journal =      {Earth\ Planet.\ Sci.\ Lett.},
  year =         2012,
  doi =          {10.1016/j.epsl.2012.04.042},
  volume =       {335-336},
  pages = 	 {226-237}
}

@Article{katz10b,
 author =     {R.F. Katz},
 title =      {Porosity-driven convection and asymmetry beneath
               mid-ocean ridges},
 journal =    {Geochem.\ Geophys.\ Geosys.},
 volume =     {10},
 number =     {Q0AC07},
 year =       {2010},
 doi =        {10.1029/2010GC003282},
}

@Article{england10,
 author =     {P.C. England and R.F. Katz},
 title =      {Melting above the anhydrous solidus controls the
               location of volcanic arcs},
 journal =    {Nature},
 year =       {2010},
 volume =     {467},
 pages =      {700--703},
 doi =        {10.1038/nature09417},
}

@Article{weatherley10,
 author =     {S. Weatherley and R.F. Katz},
 title =      {Plate-Driven Mantle Dynamics and Global Patterns of
               Mid-Ocean Ridge Bathymetry},
 journal =    {Geochem.\ Geophys.\ Geosys.},
 year =       {2010},
 volume =     {11},
 number =     {10},
 doi =        {10.1029/2010GC003192},
}
@Article{katz10,
 author = 	 {R.F. Katz and M.G. Worster},
 title = 	 {The stability of ice-sheet grounding lines},
 journal = 	 {Proc.~Roy.~Soc.~A},
 year = 	 {2010},
 volume = 	 {466},
 pages = 	 {1597--1620},
 doi =          {10.1098/rspa.2009.0434},
 url = {http://www.earth.ox.ac.uk/~richardk/publications/Katz_Worster_PRSA10.pdf}
}
@article{kyrkesmith2013stress,
  title={Stress balances of ice streams in a vertically integrated, higher-order formulation},
  author={Kyrke-Smith, T.M. and Katz, R.F. and Fowler, A.C.},
  journal={Journal of Glaciology},
  volume={59},
  number={215},
  pages={449--466},
  year={2013},
  doi = {10.3189/2013JoG12J140}
}
@Article{takei2013anisotropy1,
  author =	 {Takei Y. and R.F. Katz},
  title =	 {{Consequences of viscous anisotropy in a deforming,
                  two-phase aggregate: 1. Governing equations and
                  linearised analysis}},
  journal =	 {J.\ Fluid\ Mech.},
  year =	 2013,
  volume =	 734,
  pages =	 {424-455},
  doi =          {10.1017/jfm.2013.482}
}
@Article{katz2013anisotropy2,
  author =	 {Katz R.F. and Y. Takei},
  title =	 {{Consequences of viscous anisotropy in a deforming,
                  two-phase aggregate: 2. Numerical solutions of the
                  full equations}},
  journal =	 {J.\ Fluid\ Mech.},
  year =	 2013,
  volume =	 734,
  pages =	 {456-485},
  doi =          {10.1017/jfm.2013.483}
}
@Article{kyrke-smith2014subglacial,
  author = 	 {Kyrke-Smith, T.M. and R.F. Katz and A.C. Fowler},
  title = 	 {Subglacial hydrology and the formation of ice streams},
  journal = 	 {Proc.\ Roy.\ Soc.\ A},
  year = 	 {2014},
  volume = 	 {470},
  number = 	 {2161},
  doi = 	 {10.1098/rspa.2013.0494}
}
@ARTICLE{SpiegelmanWilsonVanKeken2013,
   author = {{Spiegelman}, M.~W. and {Wilson}, C.~R. and {Van Keken}, P.~E.
	},
    title = "{TerraFERMA: The Transparent Finite Element Rapid Model Assembler for multi-physics problems in the solid Earth sciences}",
  journal = {AGU Fall Meeting Abstracts},
 keywords = {0560 COMPUTATIONAL GEOPHYSICS Numerical solutions, 1902 INFORMATICS Community modeling frameworks, 1906 INFORMATICS Computational models, algorithms},
     year = 2013,
    month = dec,
    pages = {A2208},
   adsurl = {http://adsabs.harvard.edu/abs/2013AGUFMDI31A2208S},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@article{bueler2009shallow,
  title={{Shallow shelf approximation as a ``sliding law'' in a thermomechanically coupled ice sheet model}},
  author={Ed Bueler and Jed Brown},
  journal={Journal of Geophysical Research-Earth Surface},
  volume={114},
  number={F3},
  pages={F03008},
  year={2009},
  publisher={American Geophysical Union}
}
@article{bueler2007est,
  title={{Exact solutions to the thermomechanically coupled shallow ice approximation: effective tools for verification}},
  author={Ed Bueler and Jed Brown and Craig Lingle},
  journal={J. Glaciol},
  volume={53},
  pages={499--516},
  year={2007}
}
@article{bueler2007fcv,
  title={{Fast computation of a viscoelastic deformable Earth model for ice-sheet simulations}},
  author={Ed Bueler and Craig S. Lingle and Jed Brown},
  journal={Ann. Glaciol},
  volume={46},
  pages={97--105},
  year={2007}
}
@article {bueler2005iso,
  author = {Ed Bueler and Craig S. Lingle and Jed A. Kallen-Brown and David N. Covey and Latrice N. Bowman},
  title = {Exact solutions and numerical verification for isothermal ice sheets},
  journal = {J. Glaciol.},
  volume = {51},
  number = {173},
  pages = {291--306},
  year = {2005},
}
@article{chao2008programming,
  title={{Programming on Numerical Simulation of Tsunami with PETSc and FEPG}},
  author={Chao-fan, Z. and Yao-lin, S.},
  journal={Earthquake},
  year={2008}
}
@article{Marti2014,
  author  = {Marti, P. and Schaeffer, N. and Hollerbach, R. and Cébron, D. and Nore, C. and Luddens, F. and Guermond, J.-L. and Aubert, J. and Takehiro, S. and Sasaki, Y. and Hayashi, Y.-Y. and Simitev, R. and Busse, F. and Vantieghem, S. and Jackson, A.},
  title   = {Full sphere hydrodynamic and dynamo benchmarks},
  journal = {Geophysical Journal International},
  year    = {2014},
  doi     = {10.1093/gji/ggt518},
  URL     = {http://gji.oxfordjournals.org/content/early/2014/01/26/gji.ggt518.abstract},
}
@inproceedings{GanFuLukYangXueYang2013,
  author = {Gan, Lin and Fu, Haohuan and Luk, Wayne and Yang, Chao and Xue, Wei and Yang, Guangwen},
  title = {Global Atmospheric Simulation on a Reconfigurable Platform},
  booktitle = {Proceedings of the 2013 IEEE 21st Annual International Symposium on Field-Programmable Custom Computing Machines},
  series = {FCCM '13},
  pages = {230--},
  year = {2013},
  isbn = {978-0-7695-4969-9},
  url = {http://dx.doi.org/10.1109/FCCM.2013.26},
  doi = {10.1109/FCCM.2013.26},
  acmid = {2495688},
  publisher = {IEEE Computer Society},
}
@inproceedings{GanFuChaoLukXueMencerHuangYang2014,
  author={Lin Gan and Haohuan Fu and Chao Yang and Luk, W. and Wei Xue and Mencer, O. and Xiaomeng Huang and Guangwen Yang},
  booktitle={Field Programmable Logic and Applications (FPL), 2014 24th International Conference on},
  title={A highly-efficient and green data flow engine for solving euler atmospheric equations},
  year={2014},
  month={Sept},
  pages={1-6},
  doi={10.1109/FPL.2014.6927462},
}
%Aagaard, B., Williams, C., Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), EarthScope National Meeting, Austin, Texas, May 17–20.
%Aagaard, B., Williams, C., and Knepley, M. (2011). PyLith: A finite-element code for modeling quasi-static and dynamic crustal deformation (abstract), Southern California Earthquake Center Annual Meeting, Palm Springs, California, September 11–14.
%Aagaard, B., Williams, C., and Knepley, M. (2012). PyLith: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation (abstract), Seismological Society of America Annual Meeting, San Diego, California, April 17-19.
@article{AagaardKnepleyWilliams13,
  title   = {A Domain Decomposition Approach to Implementing Fault Slip in Finite-Element Models of Quasi-static and Dynamic Crustal Deformation},
  author  = {Brad T. Aagaard and Matthew G. Knepley and Charles A. Williams},
  journal = {Journal of Geophysical Research: Solid Earth},
  volume  = {118},
  number  = {6},
  pages   = {3059--3079},
  issn    = {2169-9356},
  url     = {http://dx.doi.org/10.1002/jgrb.50217},
  note    = {\url{http://dx.doi.org/10.1002/jgrb.50217}},
  doi     = {10.1002/jgrb.50217},
  keywords = {fault slip, finite-element modeling, crustal deformation, earthquake physics},
  year    = {2013}
}

@inproceedings{AagaardKnepleyWilliams11,
  author       = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
  title        = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  note         = {Fall Meeting Supplemental, Abstract DI14A-08},
  year         = {2011}
}
@inproceedings{Knepley10b,
  author       = {Matthew G. {Knepley}},
  title        = {Acceleration of low order finite element computation with {GPUs} (Invited)},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  note         = {Fall Meeting Supplemental, Abstract IN44A-01},
  year         = {2010}
}

@inproceedings{MayKnepleyGurnis09,
  author       = {Dave A. May and Matthew G. Knepley and Michael Gurnis},
  title        = {{CitcomSX}: Robust preconditioning in {CitcomS} via {PETSc}},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  note         = {Fall Meeting Supplemental, Abstract P31A-A1241},
  year         = {2009}
}
@inproceedings{YuenKnepleyErlebacherWright09,
  author       = {David A. Yuen and Matthew G. Knepley and Gordon Erlebacher and Grady B. Wright},
  title        = {The Coming Role of {GPU} in Computational Geodynamics},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  note         = {Fall Meeting Supplemental, Abstract DI22A-05},
  year         = {2009}
}
@inproceedings{AagaardKnepleyWilliams08,
  author       = {Brad Aagaard and Charles A. Williams and Matthew G. Knepley},
  title        = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  volume       = {89},
  number       = {53},
  note         = {Fall Meeting Supplemental, Abstract T41A-1925},
  year         = {2007}
}
@inproceedings{AagaardKnepleyWilliams07,
  author       = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
  title        = {{PyLith}: A Finite-Element Code for Modeling Quasi-Static and Dynamic Crustal Deformation},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  volume       = {88},
  number       = {52},
  note         = {Fall Meeting Supplemental, Abstract T21B-1798},
  year         = {2007}
}
@inproceedings{AagaardKnepleyWilliams05,
  author       = {Charles A. Williams and Brad Aagaard and Matthew G. Knepley},
  title        = {Development of software for studying earthquakes across multiple spatial and temporal scales by coupling quasi-static and dynamic simulations},
  booktitle    = {Eos Transactions of the AGU},
  organization = {American Geophysical Union},
  volume       = {86},
  number       = {52},
  note         = {Fall Meeting Supplemental, Abstract S53A-1072},
  year         = {2005}
}
@inproceedings{WilliamsGableHagerMeadeAagaardKnepley08,
  author    = {Charles A. Williams and Carl Gable and Bradford H. Hager and Brendan Meade and Brad Aagaard and Matthew G. Knepley},
  title     = {Modeling of Multiple Earthquake Cycles in Southern California Using the {SCEC} Community Fault Model},
  booktitle = {Proceedings of Geosciences '08},
  address   = {Wellington, NZ},
  month     = {November},
  year      = {2008}
}
@techreport{Zhang07,
  title       = {Two New Approaches in Solving the Nonlinear Shallow Water Equations for Tsunamis},
  author      = {C. Zhang and M. G. Knepley and D. A. Yuen and Y. Shi},
  type        = {Preprint},
  number      = {ANL/MCS-P1459-0907},
  institution = {ANL},
  month       = {September},
  year        = {2007}
}
@Article{katz08b,
 author =     {Richard F. Katz},
 title =      {Magma dynamics with the enthalpy method: {B}enchmark solutions and magmatic focusing at mid-ocean ridges},
 journal =    {J. Petrology},
 year =       {2008},
 volume =     {49},
 pages =      {2099--2121},
 doi =        {10.1093/petrology/egn058}
}
@article{hgrhkjvv2008,
title = "On preconditioning for a parallel solution of the Richards equation",
author = "Michael Herbst and Swen Gottschalk and Martin Reissel and Horst Hardelauf and Roy Kasteel and Matthieu Javaux and Jan Vanderborght and Harry Vereeckena",
journal = "Computers and Geosciences",
volume = "34",
pages = "1958--1963",
year = "2008",
}
@article{MayMoresi2008,
title = "Preconditioned iterative methods for {Stokes} flow problems arising in computational geodynamics",
journal = "Physics of the Earth and Planetary Interiors",
volume = "171",
number = "1-4",
pages = "33--47",
year = "2008",
note = "{R}ecent Advances in Computational Geodynamics: Theory, Numerics and Applications",
issn = "0031-9201",
doi = "DOI: 10.1016/j.pepi.2008.07.036",
url = "http://dx.doi.org/10.1016/j.pepi.2008.07.036",
author = "Dave A. May and Louis Moresi",
keywords = {Stokes flow, Krylov, Preconditioner, Schur complement, BFBt}
}
@article{KausMuhlhausMay2010,
  title   = {A stabilization algorithm for geodynamic numerical simulations with a free surface},
  author  = {Boris JP Kaus and Hans M{\"u}hlhaus and Dave A May},
  journal = {Physics of the Earth and Planetary Interiors},
  volume  = {181},
  number  = {1},
  pages   = {12--20},
  year    = {2010},
}
@article{DuretzMayGeryaTackley2011,
  title   = {Discretization errors and free surface stabilization in the finite difference and marker-in-cell method for applied geodynamics: A numerical study},
  author  = {Thibault Duretz and David Alexander May and Taras V Gerya and Paul J Tackley},
  journal = {Geochemistry, Geophysics, Geosystems},
  volume  = {12},
  number  = {7},
  year    = {2011},
}
@article{FuruichiMayTackley2011,
  title   = {Development of a {Stokes} flow solver robust to large viscosity jumps using a {Schur} complement approach with mixed precision arithmetic},
  author  = {Mikito Furuichi and Dave A May and Paul J Tackley},
  journal = {Journal of Computational Physics},
  volume  = {230},
  number  = {24},
  pages   = {8835--8851},
  year    = {2011},
}
@article{KellerMayKaus2013,
  title   = {Numerical modelling of magma dynamics coupled to tectonic deformation of lithosphere and crust},
  author  = {Tobias Keller and Dave A May and Boris JP Kaus},
  journal = {Geophysical Journal International},
  volume  = {195},
  number  = {3},
  pages   = {1406--1442},
  year    = {2013},
}
@article{SchellartFreemanStegmanMoresiMay2007,
  title   = {Evolution and diversity of subduction zones controlled by slab width},
  author  = {WP Schellart and Justin Freeman and David R Stegman and Louis Moresi and David A May},
  journal = {Nature},
  volume  = {446},
  number  = {7133},
  pages   = {308--311},
  year    = {2007},
}
@article{CrameriSchmelingGolabekDuretzOrendtBuiterMayKausGeryaTackley2012,
  title   = {A comparison of numerical surface topography calculations in geodynamic modelling: an evaluation of the sticky air method},
  author  = {F Crameri and H Schmeling and GJ Golabek and T Duretz and R Orendt and SJH Buiter and David A May and Boris JP Kaus and Taras V Gerya and Paul J Tackley},
  journal = {Geophysical Journal International},
  volume  = {189},
  number  = {1},
  pages   = {38--54},
  year    = {2012},
}
@article{StegmanFreemanSchellartMoresiMay2006,
  title   = {Influence of trench width on subduction hinge retreat rates in 3-D models of slab rollback},
  author  = {David R Stegman and Justin Freeman and WP Schellart and Louis Moresi and David A May},
  journal = {Geochemistry, Geophysics, Geosystems},
  volume  = {7},
  number  = {3},
  year    = {2006},
}
@inproceedings{may2014ptatin,
  title     = {{pTatin3D}: {H}igh-performance methods for long-term lithospheric dynamics},
  author    = {Dave A May and Jed Brown and Laetitia {Le Pourhiet}},
  booktitle = {Proceedings of {SC14}: The {International Conference for High Performance Computing, Networking, Storage and Analysis}},
  organization = {ACM},
  pages     = {274--284},
  year      = {2014},
  doi       = {10.1109/SC.2014.28},
}
@article{MayBrownPourhiet2015,
  title   = {A scalable, matrix-free multigrid preconditioner for finite element discretizations of heterogeneous {Stokes} flow},
  author  = {David A May and Jed Brown and Laetitia {Le Pourhiet}},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {290},
  pages   = {496--523},
  year    = {2015},
  doi     = {10.1016/j.cma.2015.03.014},
}
@article{DuretzMayYamato2016,
  title   = {A free surface capturing discretization for the staggered grid finite difference scheme},
  author  = {Thibault Duretz and Dave A May and Philippe Yamato},
  journal = {Geophysical Journal International},
  volume  = {204},
  number  = {3},
  pages   = {1518--1530},
  year    = {2016},
}
@article{RhebergenWellsKatzWathen2014,
  author  = {Sander Rhebergen and Garth N. Wells and Richard F. Katz and Andrew J. Wathen},
  title   = {Analysis of block-preconditioners for models of coupled magma/mantle dynamics},
  journal = {SIAM J. Sci. Comput.},
  volume  = {36},
  pages   = {A1960--A1977},
  year    = {2014},
}
@Article{katz08a,
 author =     {R.F. Katz and M.G. Worster},
 title =      {Simulation of directional solidification, thermochemical convection, and chimney formation in a {H}ele-{S}haw cell},
 journal =    {J. Comp. Phys.},
 volume =     {227},
 pages =      {9823-9840},
 year =       {2008},
 doi =        {10.1016/j.jcp.2008.06.039}
}
@Article{aabg2007,
  author  = {A. Askan and V. Akcelik and J. Bielak and O. Ghattas},
  title   = {Full waveform inversion for seismic velocity and anelastic losses in heterogeneous structures},
  journal = {Bulletin of Seismological Society of America},
  year    = {2007},
  volume  = {97},
  pages   = {1990--2008}
}
@Article{katz2006,
  author  = {Richard F. Katz and Marc Spiegelman and Benjamin Holtzman},
  title   = {The dynamics of melt and shear localization in partially molten aggregates},
  journal = {Nature},
  year    = {2006},
  volume  = {442},
  pages   = {676--679},
  month   = {August},
  day     = {10},
  url     = {http://www.nature.com/nature/journal/v442/n7103/abs/nature05039.html}
}
@InProceedings{mqrs2003,
  author = "Roland Masson and Philippe Quandalle and Stephane Requena and Robert Scheichl",
  year   = "2003",
  title  = "Parallel Preconditioning for Sedimentary Basin Simulations",
  booktitle = "Large-Scale Scientific Computing: 4th International Conference, LSSC 2003, Sozopol, Bulgaria, June 4-8, 2003"
}
@InProceedings{lichtner1,
  author = "Chuan Lu and Peter C. Lichtner",
  year   = "2005",
  title  = "{PFLOTRAN}: Massively Parallel {3-D} Simulator for {CO2} Sequestration in Geologic Media",
  booktitle = "Fourth Annual Conference on Carbon Capture and Sequestration DOE/NETL",
 Lab = {LANL}
}
@Article{smw2003,
  author =	 {R.  Scheichl and R.  Masson and J.  Wendebourg},
  title =	 {Decoupling and Block Preconditioning for Sedimentary Basin Simulations},
  journal =	 {Computational Geosciences},
  year =	 {2003},
  volume =	 {7},
  pages =	 {295--318},
  url = {http://www.maths.bath.ac.uk/MATHEMATICS/preprints.html}
}
@Article{kees-miller-03,
  author =	 {C. E. Kees and C.T. Miller and E.W. Jenkins and C.T. Kelley},
  title =	 {Versatile multilevel Schwarz preconditioners for multiphase flow},
  journal =	 {Computational Geosciences},
  year =	 {2003},
  volume =	 {7},
  pages =	 {91--114}
}
@Article{bk2003,
  author =	 {JN Buur and T Kuehnel},
  title =	 {Improving depth imaging by automated model updating},
  journal =	 {The Leading Edge},
  year =	 {2003},
  volume =	 {22},
  pages =	 {310-318}
}
@article{FrederickBuffett2016,
  title   = {Submarine groundwater discharge as a possible formation mechanism for permafrost-associated gas hydrate on the circum-Arctic continental shelf},
  author  = {Jennifer M. Frederick and Bruce A. Buffett},
  journal = {Journal of Geophysical Research: Solid Earth},
  volume  = {121},
  number  = {3},
  pages   = {1383--1404},
  issn    = {2169-9356},
  url     = {http://dx.doi.org/10.1002/2015JB012627},
  doi     = {10.1002/2015JB012627},
  year    = {2016},
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML:Simulation of the earth's mantle and crust is valuable to
% LiteralHTML:understanding earthquakes, volcanos, etc. PETSc has been used for a
% LiteralHTML:variety of these simulations.</p>
% LiteralHTML:</font>
% LiteralHTML:
@InProceedings{appelbe1,
  author = "B. Appelbe and D. May and S. Quenette and S. Tang and  F. Wang and L. Moresi",
  year   = "2003",
  title  = "Mantle convection modeling with viscoelastic/brittle lithosphere:
            Numerical and computational methodology",
  page = "781",
  booktitle = "Lecture Notes in Computer Science, volume 2659, part of the ICCS Conference Proceedings",
  publisher = "Springer-Verlag",
  URL = "http://vpac.org/VDT/SNARK/Presentations/RD0201-paper-20030602-ICCS03_ACES03_LNCS-mantle_convection_modelling.pdf"
}
% LiteralHTML:<a name="katz">
@InProceedings{gd1,
 Author      = "Guillaume Dumont and Michel Kern",
 TITLE       = "Parallelization of a 3D Seismic Migration Code with PETSc",
 year        = 1999,
 booktitle   = "Proceedings of the Ninth SIAM Conference on Parallel Processing for Scientific Computing"
}
% LiteralHTML: <center><img  alt="" src="images/katz1.jpg">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<img  alt="" src="images/katz3.jpg">
% LiteralHTML: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<img  alt="" src="images/katz2.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML: Figures from the work of Richard Katz
@PhdThesis{KatzThesis,
  author =       {R.F. Katz},
  title =        {The deep roots of volcanoes: models of magma
                  dynamics with applications to subduction zones},
  school =       {Columbia University},
  year =         {2005},
  url = {http://www.ldeo.columbia.edu/\~{ }katz/thesis/Katz_Dissertation_Columbia05.pdf}
}
@incollection{KnepleyKatzSmith06,
   author = {Knepley, Matthew G. and Katz, Richard F. and Smith, Barry},
   affiliation = {Argonne National Laboratory Mathematics and Computer Science Division Argonne IL USA},
   title = {Developing a Geodynamics Simulator with {PETSc}},
   booktitle = {Numerical Solution of Partial Differential Equations on Parallel Computers},
   series = {Lecture Notes in Computational Science and Engineering},
   editor = {Bruaset, Are Magnus and Tveito, Aslak},
   publisher = {Springer Berlin Heidelberg},
   isbn = {978-3-540-31619-0},
   keyword = {Mathematics and Statistics},
   pages = {413-438},
   volume = {51},
   url = {http://dx.doi.org/10.1007/3-540-31619-1_12},
   note = {10.1007/3-540-31619-1\_12},
   year = {2006}
}
@Article{Katz04,
  author =	 {Richard F. Katz and Marc Spiegelman and S.M. Carbotte},
  title =	 {Ridge migration, asthenospheric flow and the origin of magmatic segmentation in the global mid-ocean
                  ridge system},
  journal =	 {Geophys.\ Res.\ Letts.},
  year =	 {2004},
  volume =	 {31},
  pages =	 {L15605},
}
@Article{Katz07,
  author  = {Richard F. Katz and Matthew G. Knepley and Barry Smith and Marc Spiegelman and Ethan Coon},
  title   = {Numerical simulation of geodynamic processes with the {Portable Extensible Toolkit for Scientific Computation}},
  journal = {Phys. Earth Planet. In.},
  volume  = {163},
  pages   = {52--68},
  year    = {2007}
}
@article{williams2006development,
  title={{Development of a package for modeling stress in the lithosphere}},
  author={Williams, CA},
  journal={Eos Trans. AGU},
  volume={87},
  pages={36},
  year={2006}
}
@Article{GoversWortel05,
 author        = {R. Govers and M.J.R. Wortel},
 title         = {Lithosphere tearing at STEP faults: response to edges of subduction zones},
 journal       = {Earth and Planetary Science Letters},
 volume        = {236/1-2},
 pages = {505-523},
 year  = {2005},
}
@InProceedings{snark2,
  author = "B. Appelbe and D. May and S. Quenette and S. Tang and  F. Wang and L. Moresi",
  year   = "2002",
  title  = "Towards Rapid Geoscience Model Development - The {Snark} Project",
  booktitle = "Proceedings of 3rd ACES (APEC Cooperation for Earthquake Simulation) Workshop"
}
@Article{snark1,
   author = "Bill Appelbe and David May and Louis Moresi and Steve Quenette and Siew-Chiang Tan and Feng Wang",
   title = "Snark - A Reusable Framwork for Geoscience Computational Models",
   journal="Submitted to Pure and Applied Geosciences"
}
@InProceedings{earthquake2003,
  author = "Volkan Akcelik and Jacobo Bielak and George Biros and Ioannis Epanomeritakis and Antonio Fernandez
            and Omar Ghattas and Eui Joong Kim and David O'Hallaron and Tiankai Tu",
  year   = "2003",
  title  = "High Resolution Forward and Inverse Earthquake Modeling on Terascale Computers",
  booktitle = "Proceedings of SC2003",
  note = "A winner of the Gordon Bell Prize for special achievement at SC2003"
}
@inproceedings{Stefano12,
  author    = {Michele De Stefano},
  title     = {Simultaneous Joint Inversion of Refraction Tomography and Magnetic Data},
  booktitle = {PIERS Proceedings},
  month     = {August},
  address   = {Moscow, RUSSIA},
  pages     = {491--495},
  year      = {2012}
}
%http://www.piers.org/piersproceedings/download.php?file=cGllcnMyMDEyTW9zY293fDJBN18wNDkxLnBkZnwxMjAzMTUwNDE2MDY=

% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML: <center><img alt=""
% LiteralHTML: src="images/ocean.jpg"></center></p>
@article{khatiwala07,
   author = "Khatiwala, S.",
   title = "A computational framework for simulation of biogeochemical tracers in the ocean",
   journal = "Glob. Biogeochem. Cycles",
   volume = "21",
   doi = "doi:10.1029/2007GB002923",
   year = 2007,
   url = " http://www.ldeo.columbia.edu/\~{ }spk/Papers/KhatiwalaMatrixBiogeochemGBC07.pdf"
 }
@Article{dks2004,
  author =        "Sergey Danilov, Gennady Kivman and Jens Schroeter",
  journal =      "Ocean Modelling",
  year = "2004",
  volume = "6(2)",
  pages = "125-150",
  title  = "A finite-element Ocean Model: Principles and Evaluation",
  url = "http://www.sciencedirect.com/science?_ob=IssueURL&_tockey=%23TOC%236214%232004%23999939997%231%23FLA%23Volume_6,_Issue_2,_Pages_101-190_(2004)&_auth=y&view=c&_acct=C000007278&_version=1&_urlVersion=0&_userid=97338&md5=c3a50a31c599d8d38c8ce1f29117f267"
}
@Article{danilov1,
author = {S. Danilov and G. Kivman and J. Schroter},
year = 2004,
title = {Evaluation of an eddy-permitting finite-element ocean model in the North Atlantic},
journal = {Ocean Modelling}
}
@Article{nerger1,
author = {L. Nerger and S. Danilov and G. Kivman and W. Hiller and J. Schroter},
year = 2004,
title = {Data Assimilation with the Ensemble Kalman Filter and the SEIK Filter applied to a Finite Element Model of the North Atlantic},
journal = {Journal of marine systems},
}
@conference{rakowsky2003self,
  title={{A self-adaptive finite element model of the atmosphere}},
  author={Rakowsky, N. and Frickenhaus, S. and Hiller, W. and L{\\"a}uter, M. and Handorf, D. and Dethloff, K. and Zwieflhofer, W. and Kreitz, N.},
  booktitle={Realizing teracomputing: proceedings of the tenth ECMWF Workshop on the Use of High Performance Computing in Meteorology: Reading, UK, 4-8 November, 2002},
  pages={279},
  isbn={981238376X},
  year={2003},
  organization={World Scientific Pub Co}
}
@Article{lauter3,
author = {M. Lauter},
year = 2004,
title = {GrossrAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell},
 journal = {Berichte zur Polar- und Meeresforschung},
}
@Article{lauter2,
author = {M. Lauter and D. Handorf and K. Dethloff},
year = 2004,
title = {Unsteady analytical solutions of the spherical shallow water equations},
journal = {Journal of computational physics}
}
@PhdThesis{lauter1,
author = {M. Lauter},
year = 2004,
title = {GrossAumige Zirkulationsstrukturen in einem nichtlinearen adaptiven AtmosphArenmodell},
institution = {UniversitAt Potsdam, 134 P., UniversitAt Potsdam}
}
@Article{frickenhaus1,
author = {S. Frickenhaus and W. Hiller and M. Best},
year = 2005,
title = {FoSSI : The Family of Simplified Solver Interfaces for the rapid development of parallel numerical atmosphere and ocean models},
journal = {Ocean Modelling},
volume = {10},
pages = {185--191}
}
@article{0266-5611-24-3-034015,
 author={I Epanomeritakis and V Ak\c{c}elik and O Ghattas and J Bielak},
 title={A Newton-CG method for large-scale three-dimensional elastic
full-waveform seismic inversion},
 journal={Inverse Problems},
 volume={24},
 number={3},
 pages={034015 (26pp)},
 url={http://stacks.iop.org/0266-5611/24/034015},
 year={2008},
 abstract={We present a nonlinear optimization method for large-scale
3D elastic full-waveform seismic inversion. The method combines outer
Gauss-Newton nonlinear iterations with inner conjugate gradient linear
iterations, globalized by an Armijo backtracking line search, solved
on a sequence of finer grids and higher frequencies to remain in the
vicinity of the global optimum, inexactly terminated to prevent
oversolving, preconditioned by L-BFGS/Frankel, regularized by a total
variation operator to capture sharp interfaces, finely discretized by
finite elements in the Lam\'{e} parameter space to provide flexibility
and avoid bias, implemented in matrix-free fashion with adjoint-based
computation of reduced gradient and reduced Hessian-vector products,
checkpointed to avoid full spacetime waveform storage, and partitioned
spatially across processors to parallelize the solutions of the
forward and adjoint wave equations and the evaluation of gradient-like
information. Several numerical examples demonstrate the grid
independence of linear and nonlinear iterations, the effectiveness of
the preconditioner, the ability to solve inverse problems with up to
17 million inversion parameters on up to 2048 processors, the
effectiveness of multiscale continuation in keeping iterates in the
basin of attraction of the global minimum, and the ability to fit the
observational data while reconstructing the model with reasonable
resolution and capturing sharp interfaces.}
}
% LiteralHTML:
% LiteralHTML:  <a name="environmental"><H3><center>Environmental -- Subsurface Flow</center></H3>
% LiteralHTML:
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML:Modeling surface flow of water is valuable for both flood control and
% LiteralHTML:agricultural and environmental reasons. For example, regenerating the
% LiteralHTML:Florida Everglades requires extensive understanding of the surface water
% LiteralHTML:characteristics over thousands of square miles. PETSc has been used
% LiteralHTML:for a variety of these simulations.</p>
% LiteralHTML:</font>
% LiteralHTML:
@article{mills2009modeling,
  title={Modeling subsurface reactive flows using leadership-class computing},
  author={Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and Mahinthakumar, G.K. and Smith, B.F.},
  journal={Journal of Physics: Conference Series},
  volume={180},
  pages={012062},
  year={2009},
  publisher={IOP Publishing}
}
@conference{mills2007simulating,
  title={{Simulating subsurface flow and transport on ultrascale computers using PFLOTRAN}},
  author={Mills, R.T. and Lu, C. and Lichtner, P.C. and Hammond, G.E.},
  booktitle={Journal of Physics: Conference Series},
  volume={78},
  pages={012051},
  year={2007},
  organization={IOP Publishing}
}
@inproceedings{mills2009,
  title={Modeling subsurface reactive flows using leadership-class computing},
  author={Mills, R.T. and Hammond, G.E. and Lichtner, P.C. and Sripathi, V. and Mahinthakmuar, G. and Smith, B.},
  booktitle={Journal of Physics: Conference Series},
  volume={180},
  pages={102062},
  year={2009},
  organization={IOP Publishing}
}
@article{guo2013parallel,
  title = "A parallel, fully coupled, fully implicit solution to reactive transport in porous media using the preconditioned {J}acobian-{F}ree {N}ewton-{K}rylov Method ",
  journal = "Advances in Water Resources ",
  volume = "53",
  number = "0",
  pages = "101 - 108",
  year = "2013",
  note = "",
  issn = "0309-1708",
  doi = "http://dx.doi.org/10.1016/j.advwatres.2012.10.010",
  url = "http://www.sciencedirect.com/science/article/pii/S0309170812002722",
  author = "Luanjing Guo and Hai Huang and Derek R. Gaston and Cody J. Permann and David Andrs and George D. Redden and Chuan Lu and Don T. Fox and Yoshiko Fujita",
  keywords = {Reactive transport, Jacobian-Free Newton-Krylov, Physics-based block preconditioner}
}
@Unpublished{stomp,
  title = 	"STOMP (Subsurface Transport Over Multiple Phases) webpage",
  url = 	"http://stomp.pnl.gov/"
}
@INPROCEEDINGS{htfc2003,
 AUTHOR=    "L. Hluchy and V.D. Tran and D.Froehlich and W.Castaings",
 TITLE=     "Methods and Experiences For Parallelizing Flood Models",
 YEAR=      "2003",
 BOOKTITLE= "Recent Advances in Parallel Virtual Machine and Message Passing Interface: 10th European PVM/MPI User's Group Meeting",
 NOTE = "Springer Lecture Notes in Computer Science, Volume 2840",
 URL = "http://www.springerlink.com/app/home/contribution.asp?wasp=2e9afcba8f614cd9a6f94a5294d1cbb0&referrer=parent&backto=issue,93,95;journal,588,1972;linkingpublicationresults,1:105633,1"
}
@inproceedings{hulchy-tran-astalos-fmsip,
 AUTHOR=    "L. Hluchy and V.D. Tran and J. Astalos and M. Dobrucky and G. T. Nguyen and D.Froehlich",
 TITLE=     "Flood Modeling System and Its Parallelization",
 YEAR=      "2002",
 BOOKTITLE= "Proceedings of the International Conference on Parallel Computing in Electrical Engineering",
 URL = "http://portal.acm.org/citation.cfm?id=824476.825951"
}
@inproceedings{gy1,
 AUTHOR=    "J. P. Gwo and G. T. Yeh",
 TITLE=     "High-Performance Simulation of Surface-Subsurface Coupled Flow and Reactive Transport at Watershed Scale",
 YEAR=      "2004",
 BOOKTITLE= "The International Conference on Computational Methods",
 URL = "http://www.sfwmd.gov/org/era/uncertainty_wkshp/GwoYeh.pdf"
}
@conference{cheng2009efficient,
  title={{An efficient parallel method for large-scale groundwater flow equation based on PETSc}},
  author={Cheng, T. and Ji, X. and Wang, Q.},
  booktitle={Information, Computing and Telecommunication, 2009. YC-ICT'09. IEEE Youth Conference on},
  pages={190--193},
  organization={IEEE}
}
@Unpublished{sfrsm,
  title = 	"The South Florida Regional Simulation Model and Hydrologic Simulation Engine",
  url = 	"http://www.sfwmd.gov/org/pld/hsm/cerp_pres/hse_num.pdf",
  note = "Simulates overland, groundwater and canal flows for south Florida. Uses
                 PETSc for its linear solves"
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@inproceedings{Bart_Omar:SC05,
  AUTHOR = {Volkan Ak{\c c}elik and George Biros and Andrei Dr{\u{a}}g{\u{a}}nescu and Omar Ghattas
           and Judith~C. Hill and Gart~G. van Bloemen Waanders},
 TITLE = {Dynamic data driven inversion for terascale simulations: real-time indentification of airborne contaminants},
 BOOKTITLE = {Proceedings of SC2005},
 ORGANIZATION = {IEEE/ACM},
 ADDRESS = {Seattle, WA},
 YEAR  ={2005},
 MONTH = {November},
 url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/sc05-inverse.pdf",
 Lab = "SNL"
}
@InProceedings{anton-krassimir-lscc,
 Author      =  {Anton Antonov and Krassimir Georgiev and Emilia Komsalova and Zahari Zlatev},
 TITLE       =   "Comparison of Two Local Refinement Methods for Large Scale Air Pollution Simulations",
 booktitle   = "Large-Scale Scientific Computing: 4th International Conference, LSSC 2003",
 volume = "2907",
 year = 2003,
 publisher = "Springer-Verlag",
 url = "http://www.springerlink.com/app/home/contribution.asp?wasp=65dfaebc36f6453d9120b8f9f86fecc5&referrer=parent&backto=issue,32,55;journal,618,2072;linkingpublicationresults,1:105633,1"
}
@INPROCEEDINGS{aa2001,
 AUTHOR=    "Anton Antonov",
 TITLE=     "Object-Oriented Framework for Large Scale Air Pollution Modeling",
 YEAR=      "2001",
 BOOKTITLE= "Large-Scale Scientific Computing : Third International Conference, LSSC 2001, Sozopol, Bulgaria",
 NOTE = "Springer Lecture Notes in Computer Science, Volume 2179",
 URL = "http://www.springerlink.com/app/home/contribution.asp?wasp=3699c48fdb764bc7a3aa0539c7bf9f1d&referrer=parent&backto=issue,25,52;journal,1243,1972;linkingpublicationresults,1:105633,1"
}
% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
 @Article{grassley-simmons-kercher-00,
author = {William E. Glassley and Ardyth M. Simmons and James R. Kercher},
year = 2000,
title = {Mineralogical heterogeneity in fractured, porous media and
          its representation in reactive transport models},
journal = {Applied Geochemistry},
volume = {17},
pages = {699--708},
Lab = {LLNL}
}
@Article{glassey-nitao-03,
author = {William E. Glassley and John J. Nitao and Charles W. Grant and James W. Johnson and Carl I. Steefel and
 	 James R. Kercher},
year = 2003,
title = {The impact of climate change on vadose zone pore waters and its implication for long-term monitoring},
journal = {Computers and Geosciences},
volume = {29},
pages = {399-411},
Lab = {LLNL}
}
@Article{steefel-depaolo-lichtner-05,
author = {Carl I. Steefel and Donald J. DePaolo and Peter C. Lichtner},
year = 2005,
title = {Reactive transport modeling: An essential tool and a new research approach for the Earth sciences},
journal = {Earth and Planetary Science Letters},
Lab = {LLNL,LANL}
}
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% LiteralHTML: <center><img  alt=""
% LiteralHTML: src="images/scalinglarge.jpg"></center></p>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML: Sample <strong>strong scaling</strong> for the LANL PFLOTRAN flow and geochemical transport suite. (Courtesy of Richard Mills, ORNL)
@inproceedings{KongStognerGastonPetersonPermannSlaughterMartineau2018,
  title     = {A General-Purpose Hierarchical Mesh Partitioning Method with Node Balancing Strategies for Large-Scale Numerical Simulations},
  author    = {Fande Kong and Roy H. Stogner and Derek R. Gaston and John W. Peterson and Cody J. Permann and Andrew E. Slaughter and Richard C. Martineau},
  booktitle = {2018 IEEE/ACM 9th Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (scalA)},
  pages     = {65-72},
  doi       = {10.1109/ScalA.2018.00012},
  month     = {Nov},
  year      = {2018}
}

@Article{km2004,
  author = "A. Keese and H. G. Matthies",
  journal = "Computers and Structures",
  year = "2005",
  volume = "83",
  pages = "1033--1047",
  title  =  "Hierarchical parallelisation for the solution of stochastic finite element equations",
  url = "http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V28-4FPDPWM-1&_user=1722207&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000053990&_version=1&_urlVersion=0&_userid=1722207&md5=89d48cd6fd5e80989372246d8dda400f"
}
@Unpublished{hvl2002,
  title = {Numerical Modeling of NAPL Source Zone Treatment},
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Lab = {LANL}
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% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
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% LiteralHTML:
% LiteralHTML:  <a name="cfd"><H3><center>CFD</center></H3>
% LiteralHTML:
@article{FarrellMitchellWechsung2018,
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@article{YangHwangCai2016,
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@article{KhanAidun2011,
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@article{mofidi2014simulations,
 author = "A. Mofidi and P. M. Carrica",
 title = "Simulations of Zigzag Maneuvers for a Container Ship with Direct Moving Rudder and Propeller",
 journal = "Computers and Fluids",
 pages = "191--203",
 year = 2014
}
@article{paik2014fluidstructure,
 author = "K. Paik and P. M. Carrica",
 title = "Fluid-Structure Interaction for an Elastic Structure Interacting with Free Surface in a Rolling Tank",
 journal = "Ocean Engineering",
 pages = "201--212",
 year = 2014
}
@article{castro2013bubble,
 author = "A. M. Castro and P. M. Carrica",
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 pages = "131--150",
 year = 2013
}
@article{carrica2013turn,
 author = "P. M. Carrica and F. Ismail and M. Hyman and S. Bhushan and F. Stern",
 title = "Turn and Zigzag Maneuvers of a Surface Combatant Using a {URANS} Approach with Dynamic Overset Grids",
 journal = "Journal of Marine Science and Technology",
 pages = "166--181",
 year = 2013
}
@article{castro2013eulerian,
 author = "A. M. Castro and P. M. Carrica",
 title = "Eulerian polydispersed modeling of bubbly flows around ships with application to {Athena} {R}/V,",
 journal = "International Shipbuilding Progress",
 pages = "403--433",
 year = 2013
}
@article{chase2013overset,
 author = "N. Chase and T. Michael and P. M. Carrica",
 title = "Overset simulations of a {Submarine} in {Towed}, {Self}-{Propelled} and {Maneuvering} {Conditions}",
 journal = "International Shipbuilding Progress",
 pages = "171--205",
 year = 2013
}
@article{sadathosseini2013wu,
 author = "H. Sadat-Hosseini and P. -C. Wu and P. M. Carrica and H. Kim and Y. Toda and F. Stern",
 title = "{CFD} Simulation and Validation of Added Resistance of {KVLCC}2 with Fixed and Free Surge Conditions in Short and Long Head Waves",
 journal = "Ocean Engineering",
 volume = "59",
 pages = "240--273",
 year = 2013
}
@article{chase2013cfd,
 author = "N. Chase and P. M. Carrica",
 title = "CFD Simulations of a Submarine Propeller and Application to Self-Propulsion of a Submarine",
 journal = "Ocean Engineering",
 pages = "68--80",
 year = 2013
}
@article{carrica2012cfd,
 author = "P. M. Carrica and H. Sadat-Hosseini and F. Stern",
 title = "CFD Analysis of Broaching for a Model Surface Combatant with Explicit Simulation of Moving Rudders and Rotating Propellers",
 journal = "Computers and Fluids 53",
 pages = "117--132",
 year = 2012
}
@article{sakamoto2012urans,
 author = "N. Sakamoto and P. M. Carrica and F. Stern",
 title = "URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 1: Verification and Validation for Forces, Moment, and Hydrodynamic Derivatives",
 publisher = "Journal of Marine Science and Technology",
 pages = "422--445",
 year = 2012
}
@article{sakamoto2012uransb,
 author = "N. Sakamoto and P. M. Carrica and F. Stern",
 title = "URANS Simulations of Static and Dynamic Maneuvering for Surface Combatant-Part 2: Analysis and Validation of Local Flow Characteristics",
 journal = "Journal of Marine Science and Technology",
 pages = "446--468",
 year = 2012
}
@article{li2012dynamic,
 author = "Y. Li and T. Xing and K. Paik and P. M. Carrica",
 title = "Dynamic Overset {CFD} Simulations of Wind Turbine Aerodynamics",
 journal = "Renewable Energy",
 pages = "285--298",
 year = 2012
}
@article{huang2012a,
 author = "J. Huang and P. M. Carrica and F. Stern",
 title = "A Method to Compute Ship Exhaust Plumes with Waves and Wind",
 journal = "International Journal for Numerical Methods in Fluids",
 pages = "160--180",
 year = 2012
}
@article{huang2012b,
 author = "J. Huang and P. M. Carrica and F. Stern",
 title = "A geometry-based level set method for curvilinear overset grids with application to ship hydrodynamics",
 journal = "International Journal for Numerical Methods in Fluids",
 pages = "494--521",
 year = 2012
}
@article{carrica2011computations,
 author = "P. M. Carrica and H. Fu and F. Stern",
 title = "Computations of self-propulsion free to sink and trim and of motions in head waves of the {KRISO} {Container} {Ship} ({KCS}) model",
 journal = "Applied Ocean Research",
 pages = "309--320",
 year = 2011
}
@article{bhushan2011scalability,
 author = "S. Bhushan and P. M. Carrica and J. Yang and F. Stern",
 title = "Scalability and Validation Study for Large Scale Surface Combatant Computations Using {CFDShip}-Iowa",
 journal = "International Journal of High Performance Computing Applications",
 pages = "466--487",
 year = 2011
}
@article{castro2011full,
 author = "A. M. Castro and P. M. Carrica and F. Stern",
 title = "Full scale self-propulsion computations using discretized propeller for the {KRISO} container ship {KCS}",
 journal = "Computers and Fluids",
 pages = "35--47",
 year = 2011
}
@article{kandasamy2011multifidelity,
 author = "M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal",
 title = "Multi-fidelity Optimization of a High-speed Foil-assisted Semi-planing Catamaran for Low Wake",
 journal = "Journal of Marine Science and Technology",
 pages = "143--156",
 year = 2011
}
@article{kandasamy2011cfd,
 author = "M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern and E. F. Campana and D. Peri and P. Osborne and J. Cote and N. Macdonald and N. de Waal",
 title = "CFD Validation Studies for a High-speed Foil-assisted Semi-planing Catamaran",
 journal = "Journal of Marine Science and Technology",
 pages = "157--167",
 year = 2011
}
@article{sadathosseini2011cfd,
 author = "H. Sadat-Hosseini and P. M. Carrica and F. Stern and N. Umeda and H. Hashimoto and S. Yamamura and A. Mastuda",
 title = "CFD System-Based and {EFD} Study of Ship Dynamic Instability Events: Surf Riding, Periodic Motion and Broaching",
 journal = "Ocean Engineering",
 pages = "88--110",
 year = 2011
}
@article{mosaviraad2010development,
 author = "M. Mosaviraad and P. M. Carrica and F. Stern",
 title = "Development and Validation of Harmonic Wave Group Single-Run Procedure for {RAO} with Comparison to Regular Wave and Transient Wave Group Procedures Using {URANS}",
 journal = "Ocean Engineering",
 pages = "653--666",
 year = 2010
}
@article{carrica2010largescale,
 author = "P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. Stern",
 title = "Large-Scale {DES} Computations of the Forward Speed Diffraction and Pitch and Heave Problems for a Surface Combatant",
 journal = "Computers and Fluids",
 pages = "1095--1111",
 year = 2010
}
@article{carrica2010selfpropulsion,
 author = "P. M. Carrica and A. M. Castro and F. Stern",
 title = "Self-Propulsion Computations Using Speed Controller and Discretized Propeller with Dynamic Overset Grids",
 journal = "Journal of Marine Science and Technology",
 pages = "316--330",
 year = 2010
}
@article{ismail2010evaluation,
 author = "F. Ismail and P. M. Carrica and T. Xing and F. Stern",
 title = "Evaluation of Linear and Non-Linear Convection Schemes on Multidimensional Non-Orthogonal Grids with Applications to {KVLCC}2 Tanker",
 journal = "International Journal of Numerical Methods in Fluids",
 pages = "850--886",
 year = 2010
}
@article{kandasamy2010integral,
 author = "M. Kandasamy and S. K. Ooi and P. M. Carrica and F. Stern",
 title = "Integral Force/Moment Waterjet Model for {CFD} Simulations",
 journal = "Journal of Fluids Engineering",
 pages = "101103",
 year = 2010
}
@article{Kirk:2014de,
author = {Kirk, Benjamin S and Stogner, Roy H and Bauman, Paul T and Oliver, Todd A},
title = {{Modeling hypersonic entry with the fully-implicit Navier--Stokes (FIN-S) stabilized finite element flow solver}},
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year = {2014},
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@article{Carracciuolo20111382,
title   = {Computational simulations of {3D} large-scale time-dependent viscoelastic flows in high performance computing environment},
journal = "Journal of Non-Newtonian Fluid Mechanics ",
volume  = "166",
number  = {23--24},
pages   = {1382--1395},
year    = "2011",
issn    = "0377-0257",
doi     = "http://dx.doi.org/10.1016/j.jnnfm.2011.08.014",
url     = "http://www.sciencedirect.com/science/article/pii/S0377025711002163",
author  = "L. Carracciuolo and D. Casaburi and L. D’Amore and G. D’Avino and P.L. Maffettone and A. Murli",
keywords = {Parallel computations, Viscoelastic flows, DEVSS-G, \{PETSc\}, Finite element method, High performance computing},
}
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  publisher={Springer-Verlag},
  keywords={PDE framework; Octree-like Cartesian grids; Computational fluid dynamics; Thermohydraulics; Two-phase flow},
  language={English}
}

@article{bpr:cfl,
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@article{Bonfiglioli_rans_2005,
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@incollection {Bonfiglioli__Carpentieri_rans_2008,
   author = {Bonfiglioli, A. and Carpentieri, B. and Sosonkina, M.},
   affiliation = {University of Basilicata Dip.to di Ingegneria e Fisica dell’Ambiente Potenza Italy},
   title = {Performance Analysis of Parallel Algebraic Preconditioners for Solving the RANS Equations Using Fluctuation Splitting Schemes},
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@incollection {Bonfiglioli__Carpentieri_ens_2007,
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@techreport{avb2008,
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 year        = 2008,
 INSTITUTION = "University of Twente, the Netherlands",
 url         = "http://eprints.eemcs.utwente.nl/11714/01/memo1863.pdf"
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 booktitle = {43rd AIAA Aerospace Sciences Meeting and Exhibit},
 year =      2005,
 url =       {http://project.seas.gwu.edu/~fsagmae/papers/AIAA_2005_0079.pdf}
}
@InProceedings{ms2006,
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 booktitle = {European Conference on Computational Fluid Dynamics: ECCOMAS CFD 2006},
 year =      2006,
 url =       {http://www.numerical.rl.ac.uk/people/marioli/Archives/ECCOMAS-CFD-2006/documents/197.pdf}
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@Article{AraujoTeixeiraCunhaGroth08,
 Author      =  {B. J. Ara\'ujo and J. C. F. Teixeira and A. M. Cunha and C. P. T. Groth},
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 journal     =  "International Journal for Numerical Methods in Fluids",
 year        = 2008,
 url         = {http://www3.interscience.wiley.com/journal/119876958/abstract?CRETRY=1&SRETRY=0}
}
@PhdThesis{a2008,
 author =        {A. Cubero},
 title =         {a parallel coupled algorithm for collocated grids and its application to Large Eddy Simulation of a turbulent wake},
 school =        {University of Zaragoza (Spain)},
 year =          2008
}
@Article{afa2007,
 Author      =  {A. Cubero and N. Fueyo},
 TITLE       =   "A Compact Momentum Interpolation Method for unsteady flows and relaxation",
 journal     =  "Numerical Heat Transfer, part B-Fundamentals",
 volume      = 56,
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 pages       = "507--529",
 year        = 2007,
 url         = {http://www.informaworld.com/smpp/content~content=a782025305~db=all~order=page}
}
@TechReport{af2007,
  title =         "Preconditioning based on a partially implicit implementation of Momentum Interpolation for coupled solvers",
  institution =  "Fluid Mechanics Group of the University of Zaragoza (Spain)",
  year =        "2007",
  author =       "A. Cubero and N. Fueyo"
}
@InCollection{Dwight2004,
 author =        {Richard Dwight},
 title =         {Robust Mesh Deformation using the Linear Elasticity Equations},
 booktitle =     {Computational Fluid Dynamics 2006},
 editor =        {H. Deconinck and E. Dick},
 publisher =     {Springer},
 year = 2006,
 url =          {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-ICCFD4-LinElastDeformation-2006.pdf}
}
@InProceedings{Dwight2006,
 author =    {Richard Dwight and Joel Brezillon},
 title =     {Effect of Various Approximations of the Discrete Adjoint on Gradient-Based Optimization},
 booktitle = {Proceedings of the 44th AIAA Aerospace Sciences Meeting and Exhibit, Reno NV. AIAA-2006-0690},
 year =      2006,
 url =       {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-AIAAReno-ApproxAdjoint.pdf}
}
@PhdThesis{Dwight2006a,
 author =        {Richard Dwight},
 title =         {Efficiency Improvements of {RANS}-Based Analysis and
                        Optimization using Implicit and Adjoint Methods on Unstructured Grids},
 school =        {School of Mathematics, University of Manchester},
 year =          2006,
 url =          {http://www.maths.man.ac.uk/\~{ }rdwight/pub/rdwight-PhDThesis-ImplicitAndAdjoint.pdf}
}
@InProceedings{lhdfrh,
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 TITLE       =   "An adaptive Lagrange-Galerkin shallow-water model on the sphere",
 booktitle   = "Workshop Proceedings Current Development in Shallow Water Models on the Sphere
March, 10-14, 2003, Munich University of Technology, German",
 year = 2003
}
@InProceedings{brios-ying-2002,
 Author      =  {George Biros and Lexing Ying and Denis Zorin},
 TITLE       =   "The Embedded Boundary Integral Method (EBI) for the Incompressible {Navier-Stokes} equations",
 booktitle   = "IABEM 2002, International Association for Boundary Element Methods, UT Austin",
 year = 2002
}
@InProceedings{mohsen-straatman-ins,
 Author      =  {S.A. Mohsen Karimian and Anthony G. Straatman},
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  title =         "Multidimensional Residual Distribution Schemes for the Pseudo-Compressible {Euler}
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  institution =  "Universita della Basilicata via della Tecnica 3",
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@inproceedings{KnepleySarinSameh99b,
  title     = {Multilevel Preconditioning for Parallel {CFD}},
  author    = {Matthew G. Knepley and Vivek Sarin and Ahmed H. Sameh},
  booktitle = {International Conference On Preconditioning Techniques For Large Sparse Matrix Problems In Industrial Applications},
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  year      = {1999}
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@InProceedings{garbey1,
 Author      =  {M. Garbey and B. Hadri and W. Shyy.},
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 booktitle   = "Aerospace Sciences Meeting and Exhibit",
 note = "Paper No. 2005-1386",
 year = 2005
}
@article{carrica2007unsteady,
  title={An unsteady single-phase level set method for viscous free surface flows},
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  journal={International Journal for Numerical Methods in Fluids},
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  year={2007},
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@Article{pctw2004,
 Author      =  {M. S. Politano and P. M. Carrica and C. Turan and L. Weber},
 TITLE       =   "A Multidimensional Two-Phase Flow Model for the Total Dissolved Gas Downstream of Spillways",
 journal ="Journal of Hydraulic Research",
 note = {accepted for publication},
 year = 2004
}
@Article{wcs2004,
 Author      =  {R. V. Wilson and P. M. Carrica and F. Stern},
 TITLE       =   "Unsteady RANS Method for Ship Motions with Application to Roll for a Surface Combatant",
 journal ="Computers and Fluids",
 note = {in press},
 year = 2004
}
@Article{cws2005,
 Author      =  {P. M. Carrica and R. V. Wilson and F. Stern},
 TITLE       =   "Unsteady RANS Simulation of the Ship Forward Speed Diffraction Problem",
 journal ="Computers and Fluids",
 note = {accepted for publication},
 year = 2005
}
@Article{chndss2010,
  Author = {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. Stern},
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@InProceedings{chnkss2008,
 Author      =  {P. M. Carrica and J. Huang and R. Noack and D. Kaushik and B. Smith and F. Stern},
 TITLE       =   "Toward Large-Scale Computations of Ship Motions with Dynamic Overset Curvilinear Grids",
 booktitle   = "Proceedings of the 27th Symposium on Naval Hydrodynamics, Seoul, Korea",
 year = 2008
}
@MastersThesis{mtj,
 Author      =  {M. T. Jozkowski},
 TITLE       =  "Application of Algebraic Multigrid Methods to the Solution of Stratified Flows About Submerged Bodies",
 school =  {The Pennsylvania State University},
year = 2005
}
@Article{pp,
 Author      =  {E. G. Paterson and L. J. Peltier},
 TITLE       =   "Detached-Eddy Simulation of High Reynolds Number Beveled-Trailing-Edge Flows and Wakes",
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 note = {In press},
 year = 2005
}
@Article{eps,
 Author      =  {B. A. Edge and E. G. Paterson and G. Settles},
 TITLE       =   "Computational Study of the Wake and Contaminant Transport of a Walking Human",
 journal ="ASME Journal of Fluids Engineering",
 note = {In press},
 year = 2005
}
@InProceedings{rp,
 Author      =  {B. Racine and E. G. Paterson},
 TITLE       =   "Computation of Maneuvering Coefficients for Non-Body-of-Revolution Submarines Using Unsteady {RANS} {CFD}",
 booktitle   = "35th AIAA Fluid Dynamics Conference and Exhibit",
 year = 2005
}
@InProceedings{etpp,
 Author      =  {B. A. Edge and M. F. Trujillo and E. G. Paterson and L. J. Peltier},
 TITLE       =  {Prediction of Forces and Moments on a Sonobuoy Configuration Using Overset Grids and DES},
 booktitle   = "7th Overset Composite Grid and Solution Technology Symposium",
 year = 2004
}
@InProceedings{pp8,
 Author      =  {E. G. Paterson and L. J. Peltier},
 TITLE       =   {Localized turbulence simulation for naval hydrodynamics:  issues in using overset refinement grids and detached-eddy simulation},
 booktitle   = "7th Overset Composite Grid and Solution Technology Symposium",
 year = 2004
}
@InProceedings{mzwp,
 Author      =  {R. Meyer and F. J. Zajackowski and W. A. Straka,and E. G. Paterson},
 TITLE       =  "Experimental and Computational Study of Cavitation Inception on Co-Flow Nozzles",
 booktitle   =   "25th Symposium on Naval Hydrodynamics",
 year = 2004
}
@InProceedings{ppph,
 Author      =  {E. G. Paterson and J. E. Poremba and L. J. Peltier and S. A. Hambric},
 TITLE       =  "A Physics-Based Simulation Methodology for Predicting Trailing-Edge Singing",
 booktitle   =  "25th Symposium on Naval Hydrodynamics",
 year = 2004
}
@InProceedings{ppd,
 Author      =  {E. G. Paterson and L. J. Peltier},
 TITLE       =  "Detached-Eddy Simulation of High Reynolds Number Trailing-Edge Flows and Wakes",
 booktitle   =  "Symposium on LES Advancements and Applications, ASME FED Summer Meeting",
 year = 2004
}
@InProceedings{bp,
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 TITLE       =  "Simulation of Steady Circulation Control for the General Aviation Circulation Control Wing",
 booktitle   =  {NASA/ONR Workshop on Circulation Control},
 year =  2004
}
@InProceedings{pb,
 Author      =  {E. G. Paterson and W. J. Baker},
 TITLE       =  "RANS and Detached-Eddy Simulation of the NCCR airfoil",
 booktitle   =  {NASA/ONR Workshop on Circulation Control},
 year =  2004
}
@InProceedings{pb3,
 Author      =  {E. G. Paterson and W. J. Baker},
 TITLE       =  "Simulation of Steady and Pulsed Circulation Controlfor Marine-Vehicle Control Surfaces",
 booktitle   =  {42nd AIAA Aerospace Sciences Meeting},
 year =  2004
}
@InProceedings{gid1,
 Author      = "G. Frank and J. D'Elia",
 TITLE       = "{CFD} Modelling of the Flow Around the {Ahmed} Vehicle Model",
 year        = 2004,
 booktitle   = "Proceedings of the 2nd Conference on Advances and Applications of GiD",
 url = "http://www.gid.cimne.upc.es/2004/papers/p216.pdf"
}
@INBOOK{b1,
 AUTHOR=    "A.Bonfiglioli",
 chapter=     "On the use of the PETSc library for unstructured {CFD} applications",
 YEAR=      "2001",
 TITLE= "Science and Supercomputing at CINECA",
 pages =    "397--400"
}
@INPROCEEDINGS{b2004,
 AUTHOR=    "L. A. Barba",
 TITLE=     "Computing high-Reynolds number vortical flows: a highly accurate method with a fully meshless formulation",
 YEAR=      "2004",
 BOOKTITLE= "International Conference on Parallel CFD, Grand Canary, May 2004",
 note = "Submitted"
}
@INPROCEEDINGS{bl2004,
 AUTHOR=    "L. A. Barba and A. Leonard",
 TITLE=     "Computation of Viscous Vortices with Fully Meshless Method",
 YEAR=      "2004",
 BOOKTITLE= "Proceedings of ICTAM meeting in Warsaw, August 2004",
 note = "Submitted"
}
@Article{vws1,
  author = 	 "B. G. M. Van Wachem and J. C. Schouten",
  title = 	 "Experimental Validation of 3-D Lagrangian VOF Model: Bubble Shape and Rise Velocity",
  institution =  "Laboratory of Chemical Reactor Engineering, Department of Chemical Engineering and Chemistry,
                  Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands",
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  volumne    = 48,
  number     = 12,
  month      = "December",
  year = 	 2002
}
@TechReport{lbam1,
  author = 	 {P. Leggiero and A. Bonfiglioli and P. Amodio and F. Mazzi},
  title = 	 {Precondizionatori paralleli  per la fluidodinamica computazionale},
  institution =  {Dipartimento Interuniversitario di Matematica Universiti degli Studi-Politecnico di Bari Italy},
  year = 	 2002,
  number =	 {25/02},
}
@Article{Kees_Miller_02,
  author =       {C. E. Kees and C. T. Miller},
  title =        {Higher Order Time Integration Methods for Two-Phase Flow},
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  year =         2002,
  volume =       25,
  number =       2,
  pages =        {159-177.}
}
@INPROCEEDINGS{lepotmeersessers2001,
 AUTHOR=    "I. Lepot and F. Meers and J.A. Essers",
 TITLE=     "Multilevel Parallel High Order Schemes for Invisid Flow Computations on 3D Unstructured Meshes",
 YEAR=      "2001",
 BOOKTITLE= "ECCOMAS Computational Fluid Dynamics Conference 2001",
 url     = "http://www.ulg.ac.be/aerodyn"
}
@INPROCEEDINGS{knepley98,
  author    = {Matthew Knepley and Denis Vanderstraeten},
  title     = {Parallel Building Blocks for Finite Element Simulations: Application to Solid-Liquid Mixture Flows},
  booktitle = {Proceedings of Parallel CFD'97},
  publisher = {Elsevier},
  pages     = {281--287},
  year      = {1998}
}
@INPROCEEDINGS{pcfd97,
 AUTHOR=    "William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri",
 TITLE=     "Parallel Implicit {PDE} Computations: Algorithms and Software",
 PUBLISHER= "Elsevier",
 YEAR=      "1998",
 BOOKTITLE= "Proceedings of Parallel CFD'97",
 pages =    "333-344"
}
@inproceedings{knepleysamehsari98,
  author    = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin},
  title     = {Parallel Simulation of Particulate Flows},
  booktitle = {Solving Irregularly Structured Problems in Parallel},
  editors   = {A. Ferreira et al},
  year      = {1998},
  series    = {Lecture Notes in Computer Science},
  volume    = {1457},
  pages     = {226--237}
}
@Article{gkmt98,
    Author = "William D. Gropp and David E. Keyes and Lois Curfman McInnes and M. D. Tidriri",
    Title  = "Globalized {N}ewton-{K}rylov-{S}chwarz Algorithms and Software
              for Parallel Implicit {CFD}",
    journal = "Int. J. High Performance Computing Applications",
    year    = 2000,
    volume  = 14,
    url     = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P788.ps.Z",
    pages   = "102-136"
}
@INPROCEEDINGS{AGKKS-SC99,
        AUTHOR = "W. K. Anderson and W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "Achieving High Sustained Performance in an Unstructured Mesh {CFD} Application",
	BOOKTITLE = {ACM/IEEE Proc. of SC 99: High Performance Networking and Computing},
        EDITOR = "",
        PUBLISHER = "",
        url     = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P776.ps.Z",
        YEAR = "1999",
        note =   {Winner of Gordon Bell Special Prize at SC 99}
}
@Article{gkks01,
    Author = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
    Title  = "High Performance Parallel Implicit {CFD}",
    journal = "Journal of Parallel Computing",
    year    = 2001,
    volume  = 27,
    pages   = "337-362",
    url     = "http://www.mcs.anl.gov/petsc-fun3d/Papers/manke.pdf"
}
@Article{cristea-sofonea-02,
author =     {Artur Cristea and Victor Sofonea},
 title =  {Finite Difference lattice Boltzmann model for Liquid Vapour Systems},
journal =  {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical Sciences, Information Sciences},
 Volume = 3,
 number = 3,
 year = 2002
}
@Article{cristea2,
author =     {Artur Cristea and Victor Sofonea},
 title =  {Two component lattice Boltzmann model with flux limiter techniques},
journal =  {Proceedings of the Romanian Academy, Series A: Mathematics, Physics, Technical Sciences, Information Sciences},
 Volume = 4,
 number = 1,
 year = 2003,
 pages = {59--64}
}
@Article{cristea1,
author =    {Artur Cristea and Victor Sofonea},
title =  {Two component lattice Boltzmann model with flux limiters},
journal = {Central European Journal of Physics},
 Volume = 2,
 number = 2,
 year = 2004,
 pages = {382--396}
}
@Article{sofnea-lamura1,
 author =    {Victor Sofonea and Antonio Lamura and Giuseppe Gonnella and Artur Cristea},
title =     {Finite-difference lattice Boltzmann model with flux limiters for liquid-vapor systems},
   journal = {Physical Review E},
   Volume = 70,
    number = 4,
   year = 2004,
   pages = {046702-1 / 046702-9}
}
@INPROCEEDINGS{gkks01b,
        AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "Latency, Bandwidth, and Concurrent Issue Limitations in High-Performance {CFD}",
        BOOKTITLE = "Proceedings of the First MIT Conference on Computational Fluid and Solid Mechanics",
        EDITOR = "",
        LOCATION = "Cambridge, MA",
        YEAR = "2001",
        month = jun,
        url   = "http://www.mcs.anl.gov/petsc-fun3d/Papers/mit01.pdf"
}
@INPROCEEDINGS{gkks00,
        AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "Understanding the Parallel Scalability of An Implicit Unstructured Mesh {CFD} Code",
        BOOKTITLE = "Proceedings of the 7th International Conference on High Performance Computing (HiPC '2000)",
        EDITOR = "",
        LOCATION = "Bangalore, India",
        YEAR = "2000",
        pages = "395--404",
        url   = "http://www.mcs.anl.gov/petsc-fun3d/Papers/hipc00.pdf"
}
@INPROCEEDINGS{gkks-sc00,
        AUTHOR = "W. D. Gropp and D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "Performance Modeling and Tuning of an Unstructured Mesh {CFD} Application",
        BOOKTITLE = "Proceedings of SC2000",
        EDITOR = "",
        PUBLISHER = "IEEE Computer Society",
        YEAR = "2000",
        URL  = "http://www.mcs.anl.gov/petsc-fun3d/Papers/sc00.pdf"
}
@INPROCEEDINGS{knepleysamehsarin99,
        AUTHOR    = {Matthew Knepley and Ahmed H. Sameh and Vivek Sarin},
        TITLE     = {Design of Large Scale Parallel Simulations},
        BOOKTITLE = {Proceedings of Parallel CFD'99},
        EDITORS   = {A. {Ecer et al.}},
        PUBLISHER = {Elsevier},
        YEAR      = {1999}
}
@INPROCEEDINGS{GKKS-PCFD99,
  AUTHOR    = {William D. Gropp and Dinesh K. Kaushik and David E. Keyes and Barry F. Smith},
  TITLE     = {Towards Realistic Performance Bounds for Implicit {CFD} codes},
  BOOKTITLE = {Proceedings of Parallel CFD'99},
  EDITORS   = {A. {Ecer et al.}},
  PUBLISHER = {Elsevier},
  URL       = {http://www.cs.odu.edu/~keyes/papers/pcfd99_gkks.pdf},
  YEAR      = {1999}
}
@INPROCEEDINGS{KKS97,
        AUTHOR = "D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "On the Interaction of Architecture and Algorithm in the
                 Domain-Based Parallelization of an Unstructured Grid
                 Incompressible Flow Code",
        BOOKTITLE = "Proceedings of the 10th International Conference on
                     Domain Decomposition Methods",
        EDITOR = "J. Mandel et al.",
        PAGES = "311--319",
        PUBLISHER = "Wiley",
        NOTE = "",
        YEAR = "1997"
}
@INPROCEEDINGS{KKS99,
        AUTHOR = "D. K. Kaushik and D. E. Keyes and B. F. Smith",
        TITLE = "{N}ewton-{K}rylov-{S}chwarz Methods for Aerodynamic Problems: Compressible
                 and Incompressible Flows on Unstructured Grids",
        BOOKTITLE = "Proceedings of the 11th International Conference on
                     Domain Decomposition Methods",
        EDITORS = "C.-H. {Lai et al.}",
        PUBLISHER = "Domain Decomposition Press, Bergen",
        url        = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P745.ps.Z",
        YEAR = "1999"
}
@INCOLLECTION{KKS97_cfd,
     AUTHOR = "D. E. Keyes and D. K. Kaushik and B. F. Smith",
     TITLE = "Perspectives for {CFD} on Petaflops Systems",
     BOOKTITLE = "CFD Review 1998",
     EDITOR = "M. Hafez and K. Oshima",
     PUBLISHER = "World Scientific, Singapore",
     PAGES = "1079--1096",
     NOTE = "",
     YEAR = "1998"
}
@Article{hm99,
 AUTHOR=    "P. D. Hovland and L. C. McInnes",
 TITLE=     "Parallel Simulation of Compressible Flow Using Automatic
             Differentiation and {PETSc}",
 year      = 2000,
 journal =  "Parallel Computing",
  url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P796.ps.Z",
 note        = "special issue of Parallel Computing on ``Parallel Computing in Aerospace''"
}

@inproceedings{CruzBarbaKnepley08,
  author    = {Felipe A. Cruz and Lorena A. Barba and Matthew G. Knepley},
  title     = {Fast Multipole Method for particle interactions: an open source parallel library component},
  booktitle = {Proceedings of ParCFD2008},
  year      = {2008},
  editor    = {Tromeur-Dervout et. al.},
  publisher = {Elsevier}
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@article{HwangCai05,
  author  = {F.-N. Hwang and X.-C. Cai},
  title   = {A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm for incompressible {Navier-Stokes} equations},
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  year    = {2005},
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@article{BarbaLeonard07,
  author  = {Lorena A Barba and Anthony Leonard},
  title   = {Emergence and evolution of tripole vortices from net-circulation initial conditions},
  journal = {Phys. Fluids},
  volume  = {19},
  pages   = {017101},
  year    = {2007},
  doi     = {http://dx.doi.org/10.1063/1.2409734}
}

@article{Barba07,
  author  = {Lorena A Barba},
  title   = {Non-shielded multipolar vortices at high Reynolds number},
  journal = {Phys. Rev. E},
  volume  = {73},
  pages   = {065303},
  year    = {2006},
  doi     = {http://dx.doi.org/10.1103/PhysRevE.73.065303}
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@article{schofield2010multi,
  title={Multi-material incompressible flow simulation using the moment-of-fluid method},
  author={Schofield, S.P. and Christon, M.A. and Dyadechko, V. and Garimella, R.V. and Lowrie, R.B. and Swartz, B.K.},
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  volume={63},
  number={8},
  pages={931--952},
  year={2010},
  publisher={Wiley Online Library}
}
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% LiteralHTML:
% LiteralHTML: article{DeGersem99,
% LiteralHTML:   author = {Ji Wng and Yu Wang and Wen-ke Hu and Jian-ke Du},
% LiteralHTML:   title  = {The high performance of finite element analysis and applications of surface acoustic waves in finite elastic solids},
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@Article{Nagler2014,
  title   = {Sound transmission through a poroelastic layered panel},
  author  = {Loris Nagler and Ping Rong and Martin Schanz and Otto von Estorff},
  journal = {Computational Mechanics},
  volume  = {53},
  number  = {4},
  pages   = {549--560},
  issn    = {1432-0924},
  doi     = {10.1007/s00466-013-0916-x},
  url     = {http://dx.doi.org/10.1007/s00466-013-0916-x},
  year    = {2014}
}
@article {sheikh2013,
author = {Sheikh, A. H. and Lahaye, D. and Vuik, C.},
title = {On the convergence of shifted {L}aplace preconditioner combined with
multilevel deflation},
journal = {Numerical Linear Algebra with Applications},
volume = {20},
number = {4},
issn = {1099-1506},
url = {http://dx.doi.org/10.1002/nla.1882},
doi = {10.1002/nla.1882},
pages = {645--662},
keywords = {Helmholtz equation, shifted Laplace preconditioner, multigrid
deflation, Fourier analysis},
year = {2013},
}
@InProceedings{silence,
 Author      = "J.M. and Alonso and G. Garcia and V. Hernandez and F.D. Denia and F.J. Fuenmayor",
 TITLE       = "A parallel  computing approach for solving the Helmholtz equation in 3D domains: Application to the
                study of acoustic behaviour of silencers",
 year        = 2004,
 booktitle   = {Eurppean Congress on Computational Methods in Applied Sciences and Engineering (ECCOMAS)}
}
@Article{DeGersem99,
  author =       "H. De Gersem and Domenico Lahaye and S. Vandewalle and K. Hameyer",
  title  =       "Comparison of Quasi Minimal Residual and Bi-Conjugate
                  Gradient Iterative Methods to Solve Complex Symmetric
                  Systems Arising from Time-Harmonic Simulations",
  journal =      "COMPEL",
  year =         "1999",
  volume =       "18",
  number =       "3",
  pages =        "298--310",
  bibdate =      ""
}
@InProceedings{widlund-wave-98,
  author = 	 {Olof B. Widlund},
  title = 	 {Schwarz Methods for {H}elmholtz's Equation},
  booktitle = 	 {Mathematical and Numerical Aspects of Wave Propagation},
  editor =	 {John A. DeSanto},
  year =	 1998,
  publisher =	 {SIAM},
  pages     =    {620--622},
  address =	 {Philadelphia},
  note =	 {Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5}
}
@InProceedings{Toselli-wave-98,
  author = 	 {Andrea Toselli},
  title = 	 {Overlapping {S}chwarz Methods for {M}axwell's Equations in Conductive Media},
  booktitle = 	 {Mathematical and Numerical Aspects of Wave Propagation},
  editor =	 {John A. DeSanto},
  year =	 1998,
  publisher =	 {SIAM},
  address =	 {Philadelphia},
  pages =	 {540--542},
  note =	 {Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5}
}
@InProceedings{mcinnes-wave-98,
  author = 	 {L. C. McInnes and R. Susan-Resiga and H. M. Atassi and D. E. Keyes},
  title = 	 {Parallel Solution of {H}elmholtz Problems using Additive {S}chwarz Methods},
  booktitle = 	 {Mathematical and Numerical Aspects of Wave Propagation},
  editor =	 {John A. DeSanto},
  year =	 1998,
  publisher =	 {SIAM},
  address =	 {Philadelphia},
  pages =	 {623--625},
  note =	 {Proceedings of the Fourth International Conference on Mathematical and Numerical Aspects of Wave Propagation, Golden, Colorado, June 1--5}
}
@InProceedings{mska98,
  author    = "L. C. McInnes and R. Susan-Resiga and D. E. Keyes  and H. M. Atassi",
  title     = "Additive {S}chwarz Methods with Nonreflecting Boundary Conditions for the
               Parallel Computation of {H}elmholtz Problems",
  booktitle = "Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods",
  editor    = "J. Mandel et al.",
  publisher = "AMS",
  pages     = "349--357",
  year      = 1998
}
@InProceedings{ccew98,
  author    = "X.-C. Cai and M. A. Casarin, Jr. and F. W. Elliott, Jr. and O. B. Widlund",
  title     = "Overlapping {S}chwarz Algorithms for Solving {H}elmholtz's Equation",
  booktitle = "Proceedings of the 10th Intl. Conf. on Domain Decomposition Methods",
  editor    = "J. Mandel et al.",
  publisher = "AMS",
  pages     = "437-445",
  year      = 1998
}
@InProceedings{ra98a,
  author    = "R. Susan-Resiga and H. M. Atassi",
  title     = "Parallel Computing Using {S}chwarz Domain Decomposition Method for Aeroacoustic Problems",
  booktitle = "Proceedings of the 4th AIAA/CEAS Aeroacoustics Conference",
  publisher = "AIAA",
  pages     = "86-96",
  note      = "AIAA paper 98-2218",
  year      = 1998
}
@InProceedings{ar98c,
  author    = "H. M. Atassi and R. Susan-Resiga",
  title     = "Parallel Computation of Harmonic Waves using Domain Decomposition,
               Part {I}: General Formulation",
  booktitle = "Proceedings of the ASME Noise Control and Acoustics Division",
  publisher = "ASME",
  note      = "NCA-25",
  pages     = "375-379",
  year      = 1998
}
@InProceedings{ra98b,
  author    = "R. Susan-Resiga and H. M. Atassi",
  title     = "Parallel Computation of Harmonic Waves using Domain Decomposition,
               Part {II}: Numerical Implementation and Applications",
  booktitle = "Proceedings of the ASME Noise Control and Acoustics Division",
  publisher = "ASME",
  note      = "NCA-25",
  pages     = "381 -388",
  year      = 1998
}
@InProceedings{cai-dd10-98,
  author =       "Xiao-Chuan Cai and Mario A. Casarin and Frank W. Elliott, Jr. and Olof B. Widlund",
  title =        "Overlapping {S}chwarz methods for solving {H}elmholtz's Equation",
  booktitle =    "Domain Decomposition Methods 10",
  editors =      "Jan Mandel and Charbel Farhat and Xiao-Chuan Cai",
  series =       "Contemporary Mathematics",
  volume =       "218",
  publisher =    "American Mathematical Society",
  address =      "Providence, Rhode Island",
  year =         "1998",
  pages =        "437--445",
}
@inproceedings{alghamdi2011petclaw,
  title     = {Pet{C}law: A Scalable Parallel Nonlinear Wave Propagation Solver for {P}ython},
  booktitle = {Proceedings of SpringSim 2011},
  publisher = {ACM},
  author    = {Amal Alghamdi and Aron Ahmadia and David I. Ketcheson and Matthew G. Knepley and Kyle T. Mandli and Lisandro Dalcin},
  year      = {2011}
}
@article{pyclaw2012,
  author  = {David I. Ketcheson and Kyle T. Mandli and Aron J. Ahmadia and Amal Alghamdi and Manuel Quezada de Luna and Matteo Parsani and Matthew G. Knepley and Matthew Emmett},
  title   = {{PyClaw}: Accessible, Extensible, Scalable Tools for Wave Propagation Problems},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {34},
  number  = {4},
  pages   = {C210--C231},
  note    = {\url{http://arxiv.org/abs/1111.6583}},
  year    = {2012}
}
% LiteralHTML:
% LiteralHTML:  <a name="optimization"><H3><center>Optimization</center></H3>
% LiteralHTML:
@article{SojkaHorakHaplaCermak2018,
  title   = {The impact of enabling multiple subdomains per MPI process in the TFETI domain decomposition method},
  author  = {Radim Sojka and David Hor{\'a}k and V{\'a}clav Hapla and Martin {\v{C}}erm{\'a}k},
  journal = {Applied Mathematics and Computation},
  volume  = {319},
  pages   = {586--597},
  year    = {2018},
}
@article{ChenCai2014,
  title   = {A parallel two-level domain decomposition based one-shot method for shape optimization problems},
  author  = {Rongliang Chen and Xiao‐Chuan Cai},
  journal = {International Journal for Numerical Methods in Engineering},
  volume  = {99},
  number  = {13},
  year    = {2014},
  doi     = {10.1002/nme.4711}
}
@PhdThesis{Prudencio2005,
  author = {Ernesto Prudencio},
  Title  = {Parallel Fully Coupled {Lagrange-Newton-Krylov-Schwarz} Algorithms and Software for Optimization Problems Constrained by Partial Differential Equations},
  school = {University of Colorado, Boulder},
  year   = {2005}
}
@Article{PrudencioCai2007,
  title   = {Parallel multilevel restricted {Schwarz} preconditioners with pollution removing for {PDE}-constrained optimization},
  author  = {Ernesto Prudencio and X. C. Cai},
  journal = {SIAM J. Sci. Comp.},
  volume  = {29},
  number  = {3},
  pages   = {964--985},
  year    = {2007}
}
@Article{PrudencioByrdCai2006,
   author = "Ernesto Prudencio and R. Byrd and X. C. Cai",
   title = "Parallel full space {SQP Lagrange-Newton-Krylov-Schwarz} algorithms for {PDE}-constrained Optimization Problems",
   journal="SIAM J. Sci. Comp.",
   Volume="27",
   pages="1305--1328",
   year="2006"
}
@inproceedings{PrudencioByrdCai2004,
  title     = {Domain decomposition methods for {PDE}-constrained optimization problems},
  author    = {Ernesto Prudencio and R. Byrd and X. C. Cai},
  booktitle = {VECPAR 2004},
  editor    = {M. Dayde and J. Dongarra and V. Hernandex and J. Palma},
  publisher = {Springer},
  pages     = {569--582},
  year      = {2004}
}
@Article{belhamadia-fortin-pcp,
   author = "Youssef Belhamadia and Andre Fortin and Eric Chamberland",
   title = "Three-dimensional anisotropic mesh adaptation for phase change problems",
   journal="Journal of Computational Physics",
   Volume="201",
   pages="753-770",
   year="2004",
   url="http://portal.acm.org/citation.cfm?id=1055817.1055834#references"
}
@Article{biros00,
   author = "George Biros and Omar Ghattas",
   title = "A {Lagrange-Newton-Krylov-Schur} Method for {PDE} Constrained Optimization",
   journal="SIAG-Opt Views and News",
   Volume="11",
   number="2",
   year="2000",
   month="august",
   url="http://www.cs.cmu.edu/\~{ }oghattas/papers/siag-opt/siag-opt.pdf"
}
@article{bmm01,
 Author      = "Steve Benson and Lois Curfman McInnes and Jorge Mor\'{e}",
 journal     = "ACM Transactions on Mathematical Software",
 TITLE       = "A case study in the performance and scalability of optimization algorithms",
 year        = 2001,
 volume      = 27,
 number      = 3,
 pages       = "361--376",
}
@inproceedings{oghattas1999,
   author = "George Biros and Omar Ghattas",
   title  = "Parallel preconditioners for {KKT} systems arising in optimal control of viscous incompressible flows",
   booktitle = "Proceedings of Parallel CFD '99, Williamsburg, Virginia, USA, May 23-26, 1999",
   url    ="http://www.cs.cmu.edu/\~{ }oghattas/papers/pcfd99/pcfd99.pdf",
   year = 1999
}
@inproceedings{hkms00,
  title = "Using Automatic Differentiation for Second-order Matrix-free Methods
          in PDE-constrained Optimization",
  author = "P. D. Hovland and D. E. Keyes and L. C. McInnes and W. Samyono",
  url = "http://www.icase.edu/\~{ }keyes/papers/ad2000.ps",
   booktitle = "Automatic Differentiation of Algorithms: From Simulation to Optimization",
   editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent Hasco\"{e}t and Uwe Naumann},
   publisher = "Springer",
   year = "2002"
}
% old version: replace with biros2005pln1
@techreport{bg011,
   author = "George Biros and Omar Ghattas",
   title = "Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver",
   institution = "Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University",
   year = "2001",
   url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks1.pdf"
}
% old version: replace with biros2005pln2
@techreport{bg012,
   author = "George Biros and Omar Ghattas",
   title = "Parallel {Lagrange-Newton-Krylov-Schur} Methods for {PDE}-Constrained Optimization. Part II: The {Lagrange-Newton} Solver,
            and its Application to Optimal Control of Steady Viscous Flows",
   institution = "Laboratory for Mechanics, Algorithms, and Computing, Carnegie Mellon University",
   year = "2001",
   url = "http://www.cs.cmu.edu/\~{ }oghattas/papers/lnks/lnks2.pdf"
}
% LiteralHTML:
% LiteralHTML:  <a name="fastmethods"><H3><center>Fast Algorithms</center></H3>
% LiteralHTML:
@inproceedings{ly2003,
  author="Lexing Ying and G. Biros and D. Zorin and H. Langston",
  title="A New Parallel Kernel-independent Fast Multipole Method",
  booktitle="Proceedings of the ACM/IEEE conference on Supercomputing 2003",
  YEAR = "2003",
  note = "Winner of the Best Student Paper at SC2003"
}
@article{YokotaBarbaKnepley10,
  author  = {Rio Yokota and L A Barba and Matthew G Knepley},
  title   = {{PetRBF} -- A parallel {O(N)} algorithm for radial basis function interpolation},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {199},
  number  = {25-28},
  pages   = {1793--1804},
  url     = {http://arxiv.org/abs/0909.5413v1},
  note    = {\url{http://arxiv.org/abs/0909.5413v1}},
  year    = {2010}
}
@article{CruzKnepleyBarba10,
  author  = {Felipe A. Cruz and Matthew G Knepley and L A Barba},
  title   = {{PetFMM} -- A dynamically load-balancing parallel fast multipole library},
  journal = {International Journal of Numerical Methods in Engineering},
  volume  = {85},
  number  = {4},
  pages   = {403--428},
  url     = {http://arxiv.org/abs/0905.2637},
  note    = {\url{http://arxiv.org/abs/0905.2637}},
  year    = {2010}
}
% LiteralHTML:
% LiteralHTML:  <a name="otherapps"><H3><center>Other Application Areas</center></H3>
% LiteralHTML:
@article{BuchanPainUmplebySmedleyStevenson2012,
  title   = {A sub-grid scale finite element agglomeration multigrid method with application to the Boltzmann transport equation},
  author  = {AG Buchan and CC Pain and AP Umpleby and RP Smedley-Stevenson},
  journal = {International Journal for Numerical Methods in Engineering},
  volume  = {92},
  number  = {3},
  pages   = {318--342},
  year    = {2012},
  publisher = {Wiley Online Library}
}
@article{MagoulesAhamedSuzuki2015,
  title   = {Green computing on graphics processing units},
  author  = {Fr{\'e}d{\'e}ric Magoul{\`e}s and Abal-Kassim Cheik Ahamed and Atsushi Suzuki},
  journal = {Concurrency and Computation: Practice and Experience},
  year    = {2015},
  publisher = {Wiley Online Library}
}
@inproceedings{YanRhodes11,
  author = {Yan, Baoqiang and Rhodes, Philip J.},
  title = {IDEA -- An API for Parallel Computing with Large Spatial Datasets},
  booktitle = {Proceedings of the 2011 International Conference on Parallel Processing},
  series = {ICPP '11},
  pages = {355--364},
  year = {2011},
  isbn = {978-0-7695-4510-3},
  numpages = {10},
  url = {http://dx.doi.org/10.1109/ICPP.2011.70},
  doi = {10.1109/ICPP.2011.70},
  acmid = {2066965},
  publisher = {IEEE Computer Society},
  address = {Washington, DC, USA},
  keywords = {cluster, parallelization, spatial dataset, dependency, data partitioning},
}
@Article{Hakansson2013MDStochasticLiouville,
  author ="Hakansson, Par and Nguyen, ThaoNguyen and Nair, Prasanth B. and Edge, Ruth and Stulz, Eugen",
  title  ="Cu(ii)-porphyrin molecular dynamics as seen in a novel EPR/Stochastic Liouville equation study",
  journal  ="Phys. Chem. Chem. Phys.",
  year  ="2013",
  volume  ="15",
  issue  ="26",
  pages  ="10930-10941",
  publisher  ="The Royal Society of Chemistry",
  doi  ="10.1039/C3CP50788B",
  url  ="http://dx.doi.org/10.1039/C3CP50788B",
}
@Article{Hakansson2011StochasticLiouville,
  author ="Hakansson, Par and Nair, Prasanth B.",
  title  ="Implicit numerical schemes for the stochastic Liouville equation in Langevin form",
  journal  ="Phys. Chem. Chem. Phys.",
  year  ="2011",
  volume  ="13",
  issue  ="20",
  pages  ="9578-9589",
  publisher  ="The Royal Society of Chemistry",
  doi  ="10.1039/C1CP20400A",
  url  ="http://dx.doi.org/10.1039/C1CP20400A",
}
@INPROCEEDINGS{wang:lee:scidac2011,
 author = "Lei Wang and Jungho Lee and Mihai Anitescu and Anter El Azab and Lois Curfman McInnes and Todd Munson and Barry Smith",
 title = "A Differential Variational Inequality Approach for the Simulation of Heterogeneous Materials",
 booktitle = "Proceedings of SciDAC 2011 Conference",
 year = 2011
}

@article{BourdinLarsenRichardson2011,
  author  = {Blaise Bourdin and Christopher Larsen and Casey Richardson},
  title   = {A time-discrete model for dynamic fracture based on crack regularization},
  journal = {International Journal of Fracture},
  volume  = {168},
  issue   = {2},
  pages   = {133--143},
  doi     = {10.1007/s10704-010-9562-x},
  url     = {http://dx.doi.org/10.1007/s10704-010-9562-x},
  year    = {2011}
}

@book{BourdinFrancfortMarigo,
  author    = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
  title     = {The Variational Approach to Fracture},
  publisher = {Springer},
  year      = {2008}
}

@article{BourdinFrancfortMarigo2008,
  author  = {Blaise Bourdin and Gilles Francfort and Jean-Jacques Marigo},
  title   = {The Variational Approach to Fracture},
  journal = {J. Elasticity},
  volume  = {91},
  issue   = {1},
  pages   = {1--148},
  url     = {http://dx.doi.org/10.1007/s10659-007-9107-3},
  year    = {2008}
}

@article{lahtinen2008spectrum,
  title={Spectrum of the non-abelian phase in Kitaev's honeycomb lattice model},
  author={Lahtinen, V. and Kells, G. and Carollo, A. and Stitt, T. and Vala, J. and Pachos, J.K.},
  journal={Annals of Physics},
  volume={323},
  number={9},
  pages={2286--2310},
  year={2008},
  publisher={Elsevier}
}
@inproceedings{roark2004discriminative,
  title={Discriminative language modeling with conditional random fields and the perceptron algorithm},
  author={Roark, B. and Saraclar, M. and Collins, M. and Johnson, M.},
  booktitle={Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics},
  pages={47},
  year={2004},
  organization={Association for Computational Linguistics}
}
@article{roark2007discriminative,
  title={Discriminative n-gram language modeling},
  author={Roark, B. and Saraclar, M. and Collins, M.},
  journal={Computer Speech \& Language},
  volume={21},
  number={2},
  pages={373--392},
  year={2007},
  publisher={Elsevier}
}
@conference{garcia2011parallel,
  title={{Parallel performance of the PETSc Krylov methods applied to linear systems of 3D nanodevice simulators}},
  author={Garcia-Rivera, A. and Valin, R. and Seoane, N. and Garcia-Loureiro, A. and Aldegunde, M.},
  booktitle={Electron Devices (CDE), 2011 Spanish Conference on},
  pages={1--4},
  organization={IEEE}
}
@conference{wesley2006parallel,
  title={{A parallel artificial neural network implementation}},
  author={Wesley-Smith, I.},
  booktitle={Proceedings of The National Conference On Undergraduate Research (NCUR)},
  year={2006}
}
@article{hcsw1,
  author = {F.-N. Hwang and  S.-R. Cai and Y.-L. Shao and J.-S. Wu},
  title = {Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann
           equation in numerical simulation of colloidal particle interactions},
  journal = {Computer Physics Communications},
  volumne = 181,
  year =  2010,
  pages = {1529--1537}
}
@article{hh1,
  author = {C.-Y. Huang and F.-N. Hwang},
  title = {Parallel pseudo-transient Newton-Krylov-Schwarz
           continuation algorithms for bifurcation analysis of incompressible sudden expansion flows},
  journal = {Applied Numerical Mathematics},
  Volume =  60,
  year = 2010,
  pages = {738--751}
}
@article{hwhw1,
  author = {F.-N. Hwang and Z.-H. Wei and T.-M. Huang and W. Wang},
  title = {A parallel additive Schwarz preconditioned Jacobi-Davidson algorithm for polynomial eigenvalue problems
           in quantum dot simulation},
  journal = {Journal of Computational Physics},
  Volume = 229,
  year =  2010,
  pages =  {2932--2947}
}
@article{wei2011parallel,
  title={{A Parallel Scalable PETSc-Based Jacobi-Davidson Polynomial Eigensolver with Application in Quantum Dot Simulation}},
  author={Wei, Z.H. and Hwang, F.N. and Huang, T.M. and Wang, W.},
  journal={Domain Decomposition Methods in Science and Engineering XIX},
  pages={157--164},
  year={2011},
  publisher={Springer}
}
@article{flores2007sequential,
  title={{Sequential and parallel resolution of the two-group transient neutron diffusion equation using second-degree iterative methods}},
  author={Flores-S{\'a}nchez, O. and Vidal, V. and Garc{\'\i}a, V. and Flores-S{\'a}nchez, P.},
  journal={High Performance Computing for Computational Science-VECPAR 2006},
  pages={426--438},
  year={2007},
  publisher={Springer}
}
@inproceedings{GordonBell09,
  author = {Dinesh Kaushik and Michael Smith and Allan Wollaber and Barry Smith and Andrew Siegel and Won Sik Yang},
  title  = {Enabling High Fidelity Neutron Transport Simulations on Petascale Architectures},
  booktitle = {ACM/IEEE Proceedings of SC2009: High Performance Networking and Computing},
  note   = {{SC'09 Gordon Bell} Prize Finalist},
  year   = {2009}
}

@article{KnepleyKarpeevDavidovitsEisenbergGillespie10,
  author  = {Matthew G. Knepley and Dmitry A. Karpeev and Seth Davidovits and Robert~S. Eisenberg and Dirk Gillespie},
  title   = {An Efficient Algorithm for Classical Density Functional Theory in Three Dimensions: Ionic Solutions},
  journal = {Journal of Physical Chemistry},
  volume  = {132},
  number  = {12},
  pages   = {124101--124111},
  url     = {http://arxiv.org/abs/0910.1531},
  year    = {2010}
}
@article{KnepleyKarpeevEisenbergGillespie09,
   author = {{Knepley}, M.~G. and {Karpeev}, D.~A. and {Eisenberg}, R.~S. and {Gillespie}, D.},
    title = {{Energetics of Calcium Selectivity: A Three-Dimensional Classical Density Functional Theory Approach}},
  journal = {Biophysical Journal},
    month = {feb},
   volume = {96},
    pages = {661},
      doi = {10.1016/j.bpj.2008.12.3494},
     year = {2009}
}
@Article{scx2008,
   author = "SUWITO AND XIAO-CHUAN CAI AND YUNPING XI",
   title = "PARALLEL FINITE ELEMENT METHOD FOR COUPLED CHLORIDE MOISTURE DIFFUSION IN CONCRETE",
   journal="INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING",
   Volume="3",
   number="4",
   year="2006",
   url="http://www.math.ualberta.ca/ijnam/Volume-3-2006/No-4-06/2006-04-06.pdf"
}
@TechReport{kdgs2008,
  year =         2008,
  school =  "Centro Internacional de Methodos Numericos en Ingenieria, Argentina",
  title =        "High Performance Simulations of Electrokinetic Flow and Transport in Microfluidic Chips",
  author =       "Pablo A. Klera and Lisandro D. Dalcin and Fabio A. Guarnieria and Mario A. Stortia",
  url =          "http://www.cimec.org.ar/ojs/index.php/cmm/article/view/1383"
}
@article {springerlink:10.1007/s10915-011-9551-x,
   author = {Schauer, Marco and Roman, Jose and Quintana-Ortí, Enrique and Langer, Sabine},
   affiliation = {Institut für Angewandte Mechanik, Technische Universität Carolo-Wilhelmina zu Braunschweig, Spielmannstraße 11, 38106 Braunschweig, Germany},
   title = {Parallel Computation of 3-D Soil-Structure Interaction in Time Domain with a Coupled FEM/SBFEM Approach},
   journal = {Journal of Scientific Computing},
   publisher = {Springer Netherlands},
   issn = {0885-7474},
   keyword = {Mathematics and Statistics},
   pages = {1-22},
   url = {http://dx.doi.org/10.1007/s10915-011-9551-x},
   note = {10.1007/s10915-011-9551-x}
}
@techreport{jj2007,
   author = "Boris Jeremic and Guanzhou Jie",
   title = "Parallel Finite Element Computations for Soil-Foundation-Structure Interaction Problems Report",
   institution = "UCD CompGeoMech 02--2007",
   year = "2007",
   url = "http://sokocalo.engr.ucdavis.edu/~jeremic/wwwpublications/CV-R23.pdf"
}
@Unpublished{Kuiper08,
  title = 	"Fast 3D frequency-dependent Radiative Transfer for Magneto-Hydrodynamics",
  author = "Rolf Kuiper",
  institution = "Max-Planck-Institute for Astronomy",
  url = "http://www.mpia.de/~kuiper/MAKEMAKE.html",
  year = 2008
}
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        YEAR      = "2007"
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@INPROCEEDINGS{sprkssl2007,
        AUTHOR = {M. A. Smith and G. Palmiotti and C. Rabiti and D. Kaushik and A. Siegel and B. Smith and E. E. Lewis},
        TITLE     = "{PNFE} Component of the {UNIC} Code",
        BOOKTITLE = "Joint International Topical Meeting on Mathematics and Computation and Supercomputing in Nuclear Applications",
        YEAR      = "2007"
}
@inproceedings{dc-oop-03,
        AUTHOR = "H. Digonnet and T. Coupez",
        TITLE     = "Object-oriented programming for fast-and-easy development of parallel
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        BOOKTITLE = "Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics",
        YEAR      = "2003"
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@INPROCEEDINGS{dc-cfm-03,
        AUTHOR = "H. Digonnet and T. Coupez",
        TITLE     = "Calcul parallele en mise en forme des materiaux",
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        AUTHOR = "H. Digonnet and  L. Silva and T. Coupez",
        TITLE     = "Parallel computation for solving efficiently viscoelastic fluid flow problems",
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        YEAR      = "2004"
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@INPROCEEDINGS{dsc-pca3fs-04,
        AUTHOR = "H. Digonnet and  L. Silva and T. Coupez",
        TITLE     = "Parallel computation applied to 3D FE simulation of polymer injection molding",
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        YEAR      = "2004"
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        AUTHOR = "H. Digonnet and O. Basset and T. Coupez and L. Silva",
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        YEAR      = "2005"
}

@article{sz2010,
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@article{zssz2006,
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@article{jmemsci,
      author  = "Bo Zhou and Adam Powell",
      title   = "Phase Field Simulations of Liquid-Liquid Demixing During Immersion Precipitation of Polymeric Membranes in 2D and 3D",
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@INPROCEEDINGS{vbde2002,
        AUTHOR = "Anke Veser and Wolfgang Breitung and Sergey Dorofeev and Alexander Efimenko",
        TITLE     = "Flame Acceleration Distance in Obstacle-Laden Tubes",
        BOOKTITLE = "Proceedings of the NINTH INTERNATIONAL CONFERENCE ON NUMERICAL COMBUSTION",
        url       = "http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf",
        YEAR      = "2002"
}
@INPROCEEDINGS{wid2005,
        AUTHOR = "Alexander I. Bobenko and Peter Schrader",
        TITLE     = "Discrete Willmore Flow",
        BOOKTITLE = "Eurographics Symposium on Geometry Processing",
        url       = "http://www.math.tu-berlin.de/\~{ }bobenko/Papers/Willmore.pdf",
        YEAR      = "2005",
        editor = "M. Desbrun and H. Pottmann"
}
@article{stj2003,
author  = "A. Scascighini and A. Troxler and R. Jeltsch",
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year    = 2003,
pages   = "339--355",
url = "http://www3.interscience.wiley.com/cgi-bin/abstract/102521480/ABSTRACT"
}
@PhdThesis{AS2001,
  author =       {ANDREA SCASCIGHINI},
  title =        {A Numerical Method for the Design of Internal Flow Configurations Based on
                  the Inverse Euler Equations},
  school =       {SWISS FEDERAL INSTITUTE OF TECHNOLOGY, ZURICH},
  year =         {2001},
  url = {http://www.sam.math.ethz.ch/\~{ }andrea/}
}
@article{hb2005,
author  = "E. McKay Hyde and Oscar P. Bruno",
journal = "Journal of Computational Physics",
volume  = 202,
title   = "A fast, higher-order solver for scattering by penetrable bodies in three dimensions",
year    = 2005,
pages   = "236--261",
url = "http://www.acm.caltech.edu/\~{ }bruno/hyde_bruno_3d_jcp.pdf"
}
@mastersThesis{d2002,
  author =       {Matthew F Dixon},
  title =        {PARALLEL SOLUTION OF HIGH ORDER FINITE DIFFERENCE SCHEMES FOR PRICING MULTI-DIMENSIONAL AMERICAN OPTIONS},
  school =       {READING UNIVERSITY},
  year =         {2002},
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@techreport{gzb,
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}
@PhdThesis{yergeau-99,
  author =       {Daniel W. Yergeau},
  title =        {A DIAL-AN-OPERATOR APPROACH TO SIMULATION OF IMPURITY DIFFUSION IN SEMICONDUCTORS},
  school =       {Stanford},
  year =         {1999},
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 YEAR=      "2000",
 BOOKTITLE= "Physor 2000 American Nuclear Society Topical Meeting on
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 url = "http://www.llnl.gov/tid/lof/documents/pdf/237860.pdf",
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author  = "A. Bonfiglioli and P. De Palma and G. Pascazio and M. Napolitano",
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title   = "An Implicit Fluctuation Splitting Scheme for Turbomachinery Flows",
year    = 2005,
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@INPROCEEDINGS{fettig-sobh-05,
 AUTHOR=    "John Fettig and Nahil Sobh and Dmitriy V. Melnikov and Jean-Pierre Leburton",
 TITLE=     "High Performance Algorithms for Scalable Spin-Qubit Circuits with Quantum Dots",
 YEAR=      "2005",
 BOOKTITLE= "Proceedings of the 5th International Conference on Linux Clusters",
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@techreport{melnikov-matagne-05,
 Author      = "Dmitriy V. Melnikov and Philippe Matagne and Jean-Pierre Leburton and
                D.G. Austing and G. Yu and S. Tarucha and John Fettig and Nahil Sobh",
 TITLE       = "Spin configurations in circular and rectangular vertical quantum dots in a magnetic
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 year        = 2005,
 Number      = "Arxiv preprint cond-mat/0506585",
 URL        = "http://arxiv.org/pdf/cond-mat/0506585"
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@INPROCEEDINGS{richard-smedley-03,
 AUTHOR=    "Richard P. Smedley-Stevenson",
 TITLE=     "PARALLEL THERMAL RADIATION TRANSPORT IN TWO DIMENSIONS",
 YEAR=      "2003",
 BOOKTITLE= "18th International Conference on Transport Theory (18 ICTT)",
 url = "http://www.iprj.uerj.br/\~{ }ricardob/Evento_Cientifico_html/poster03j.pdf"
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@article{guan-godoy-ravaioli-03,
author  = "D. Guan and A. Godoy and U. Ravaioli and F. Gamiz",
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title   = "Comparison Between Non-Equilibrium Green's Function and Monte Carlo Simulations for
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year    = 2003,
pages   = "335--339"
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@article{OvtchinnikovCai04,
author  = "S. Ovtchinnikov and X.-C. Cai",
journal = "Numer. Lin. Alg. Applics",
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year    = 2004,
pages   = "867--881"
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@article{mixedstress,
title   = "Floating Solids: Combining Phase Field and Fluid-Structure Interactions",
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@Article{dhh2005,
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  year =       {2005},
}
@Article{dhh2004,
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  title =      {Finite element modelling of ion convection by electrostatic forces},
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  year =       {2004},
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@Article{Adams-07b,
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@INPROCEEDINGS{wc2004,
 AUTHOR=    "A. Wheelock and D. Cooke",
 TITLE=     "Computational Modeling of Ion Beam-Neutralizer Interactions in Two and Three Dimensions",
 YEAR=      "2004",
 BOOKTITLE= "40th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit",
 URL = "http://www.aiaa.org/content.cfm?pageid=406&gTable=Paper&gID=19282"
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 AUTHOR=    "Jeremie Allard and Valerie Gouranton and Emmanuel Melin and Bruno Raffin",
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 NOTE = "Resin Transfer Modeling"
}
@techreport{b2000,
 Author      = "Rickard Bergstrom",
 TITLE       = "Least-Squares Finite Element Methods for Electromagnetic Applications",
 year        = 2000,
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@article{fs2004,
  author =       {Petri Fast and Michael J. Shelley},
  title =        {A Moving Overset Grid Method for Interface Dynamics Applied to Non-Newtonian Hele Shaw Flow},
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@mastersthesis{wallach,
  author = "Hanna Wallach",
  title =  "Efficient Training of Conditional Random Fields",
  school = "University of Edinburgh",
  year = "2002",
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}
@article{something,
  author =       {T Rylander and A Bondeson},
  title =        {Stability of explicit-implicit hybrid time-stepping schemes for Maxwells equations},
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  year =         2002,
  volume = {179},
  pages = {426-438}
}
@techreport{uf1,
 Author      = "Uwe Fabricius",
 TITLE       = "Comparison of two implementations of AMG-preconditioned CG considering an electrostatic problem",
 year        = 2004,
 INSTITUTION = "Friedrich Alexander Universitat Erlangen Nurnberg Germany",
 URL        = "http://www10.informatik.uni-erlangen.de/de/Publications/TechnicalReports/TechRep04-1.pdf",
 number = "04-1"
}
@INBOOK{sg1,
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 chapter     = "Analysis of Parallel Numerical Libraries to Solve the 3D Electron Continuity Equation",
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 title = "Lecture Notes in Computer Science",
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@article{NikYilmazGiviSheikhiPope10,
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  number  = {7},
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  year    = {2010}
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@article{NikYilmazSheikhiGivi10,
  author  = {Mehdi B. Nik and Server L. Yilmaz and Mohammad Reza H. Sheikhi and Peyman Givi},
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  journal = {Flow, Turbulence and Combustion},
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  year    = {2010}
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@article{idema2013towards,
title={Towards faster solution of large power flow problems},
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number={4},
pages={4918--4925},
year={2013},
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@ARTICLE{6026245,
author={Idema, R. and Lahaye, D.J.P. and Vuik, C. and Van der Sluis, L.},
journal={Power Systems, IEEE Transactions on},
title={Scalable Newton-Krylov Solver for Very Large Power Flow Problems},
year={2012},
month={Feb},
volume={27},
number={1},
pages={390-396},
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@book{idema2014computational,
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@phdthesis{Abhyankar2011thesis,
  author = {Shrirang Abhyankar},
  title = {Development of an implicitly coupled electromechanical and electromagnetic transients simulator for power systems},
  school = {Illinois Institute of Technology},
  year = 2011
}
@InProceedings{AbhyankarHiPCNA11-1,
  author = {Shrirang Abhyankar and Barry Smith and Hong Zhang and A. Flueck},
  title =  {Using {PETSc} to develop scalable applications for next-generation power grid},
  year = 2011,
  booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid},
  url       = "http://www.mcs.anl.gov/uploads/cels/papers/P1957-0911.pdf",
  publisher = {ACM}
}
@InProceedings{AbhyankarHiPCNA11-2,
  author = {Shrirang Abhyankar and Alexander Flueck and Xu Zhang and Hong Zhang},
  title =  {Development of a parallel three-phase transient stability simulator for power systems},
  year = 2011,
  booktitle = {Proceedings of the 1st International Workshop on High Performance Computing, Networking and Analytics for the Power Grid},
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@InProceedings{AbhyankarPESGeneral2012,
  author = {Shrirang Abhyankar and A. Flueck},
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  publisher = {IEEE}
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@article{IdemaLahayeVuikSluis2012,
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@article{KorresTzavellasGalinas2013,
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  url     = "http://www.sciencedirect.com/science/article/pii/S0378779613000965",
}

% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
% LiteralHTML:<font color="#FF0000">
% LiteralHTML: Material failure, for example, cracking of steel beams resulting
% LiteralHTML: in bridge collapse and corrosion, is a little understood phenomena. Thus simulations
% LiteralHTML: are important for prediction and prevention. PETSc has been used
% LiteralHTML: in  a variety of studies of material failure.</p>
% LiteralHTML:</font>
% LiteralHTML:
@InProceedings{gray2,
 Author      = "Yuan He and Joshua Gray and Richard Braatz and Richard Alkire",
 TITLE       = "Modulized Coupled Simulation of Localized Pit Initiation in Stainless Steel",
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 booktitle   = {American Institute of Chemical Engineers 2004 Annual Meeting}
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@InProceedings{gray1,
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 year        = 2003,
 booktitle   = "Abstracts of the Electrochemical Society 204th meeting"
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@INPROCEEDINGS{crack2,
        AUTHOR = "Erin Lesulauro and Anthony R. Ingraffea and Gerd Heber and Paul A. Wawrzynek",
        TITLE     = "A multiscale modeling approach to crack initiation in metallic polycrystals",
        BOOKTITLE = "44th AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference",
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        YEAR      = "2003"
}
@techreport{hdams1,
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@inproceedings{ihwi,
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 year = 2002,
 URL        = "http://www.cfg.cornell.edu/\~{ }erin/erin/ices02_iesulauro.pdf"
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@INPROCEEDINGS{crack,
        AUTHOR = "Bruce Carter and Chuin-Shan Chen and L. Paul Chew and Nikos Chrisochoides and Guang R. Gao and
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        YEAR      = "2000"
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% LiteralHTML: <td width="100%" colspan="2"><hr size="4" color="#FF5B5B"> </td>
@techreport{defordheld1,
 Author      = "JF DeFord and BL Held",
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 year        = 2002,
 INSTITUTION = "Simulation Technology and Applied Research",
 URL        = "http://www.staarinc.com/support/papers/aces2002.pdf",
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}
@PhdThesis{Sande2003,
  author =       {Hans Vande Sande},
  title =        {Modelling and Finite Element Simulation of Non-Linear and Anisotropic Quasi-Static Electromagnetic Systems},
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  year =         2003
}
@article{sdchh2004,
  author =       {H. Vande Sande and W. Deprez and J. De Coster and F. Henrotte and K. Hameyer},
  title =        {Reducing the Computation Time of Non-Linear Problems by an Adaptive Linear System Tolerance},
  journal =      {IEEE Transactions on Magnetics},
  year =         2004,
  volume = {40},
  pages = {1306--1309}
}
@Article{Holst-Lindblom-etal:2004,
 author =      {Michael Holst and Lee Lindblom and Robert Owen and
                 Harald P. Pfeiffer and Mark A. Scheel and
                 Lawrence E. Kidder},
 title =      {Optimal constraint projection for hyperbolic evolution systems
},
 journal =      {Phys. Rev. D},
 year =      2004,
 volume =     70,
 pages =     084017
}
@Article{marm2005,
 author =      {Matthew Anderson  and Richard A. Matzner},
 title =      {Extended Lifetime in Computational Evolution of Isolated Black Holes},
 journal =  {Foundations of Physics},
 volume =  35,
 pages =     {1572--9516},
 year =      2005
}
@Article{Cook-Pfeiffer:2004,
 author =      {Cook, Gregory B. and Pfeiffer, Harald P.},
 title =      {Excision boundary conditions for black hole initial data},
 journal =  {Phys. Rev. D},
 volume =  70,
 pages =     {104016--24},
 year =      2004
}
@Article{Pfeiffer-Kidder-etal:2005,
 author =      {Harald P. Pfeiffer and Lawrence E. Kidder and Mark A. Scheel and Deirdre Shoemaker},
 title =      {Initial data for {E}instein's equations with superposed gravitational waves},
 journal =    {Phys. Rev. D},
 year =      2005,
 volume =       {71},
 pages =        {024020}
}
@Article{Pfeiffer-Kidder-etal:2003,
  author =       {Pfeiffer, Harald P. and Kidder, Lawrence E. and Scheel, Mark A. and Teukolsky, Saul A.},
  title =        {A multidomain spectral method for solving elliptic equations},
  journal =      "CPC",
  year =         2003,
  volume = {152},
  pages = {253--273},
  note = {Solves nonlinear coupled 3-D elliptic equations that arise in general relativity. For a related online version, see arXiv:gr-qc/0202096}
}
@Article{Pfeiffer-Cook-Teukolsky:2002,
  author =       {Pfeiffer, Harald P. and Cook, Gregory B. and Teukolsky, Saul A.},
  title =        {Comparing initial-data sets for binary black hole},
  journal =      "PRD",
  year =         {2002},
  volume =       {66},
  pages =        {024047},
  note =         {for a related online version, seearXiv:gr-qc/0203085}
}
@PhdThesis{Pfeiffer:2003,
  author =       {Pfeiffer, Harald P.},
  title =        {Initial Data for Black Hole Evolutions},
  school =       {Cornell University},
  year =         2003
}
@techreport{h1,
 Author      = "Erik Schnetter",
 TITLE       = "A fast apparent horizon algorithm",
 year        = 2002,
 Number      = "Arxiv preprint gr-qc/0206003",
 URL        = "http://arxiv.org/pdf/gr-qc/0206003"
}
@article{h2,
 Author      = "Erik Schnetter",
 TITLE       = "Finding apparent horizons and other 2-surfaces of constant expansion",
 year        = 2003,
 journal     = "Class. Quantum Grav.",
 pages       = "4719-4737",
 volume      = 20,
 URL        = "http://www.iop.org/EJ/article/0264-9381/20/22/001/cqg3_22_001.pdf"
}

@article{Adams-03a,
	Author = {Adams, M.~F.},
	Journal = {Numerical Linear Algebra with Applications},
	Number = {2-3},
	Pages = {141-153},
	Title = {Algebraic multigrid methods for constrained linear systems with applications to contact problems in solid mechanics},
	Volume = {11},
	Year = {2004}
}
@Article{vandesande1,
  author =        "H. Vande Sande and H. De Gersem and F. Henrotte and K. Hameyer",
  journal =      "IEEE TRANSACTIONS ON MAGNETICS",
  year = "2003",
  volume = "39",
  pages = "1709--1712",
  title  =  "Solving Nonlinear Magnetic Problems Using Newton Trust Region Methods"
}
@InProceedings{vbde1,
  author = "Rajesh Rawat and Jennifer P. Spinti and Wing Yee and Philip J. Smith",
  year   = "2002",
  title  = "Parallelization and Integration of a Large Scale Hydrocarbon Pool Fire in the Uintah PSE",
  booktitle = "In Proceedings of Ninth Internation Conference on Numerical Combustion - ICNC 2002",
  pages  = "49-55",
  url    = "http://web.ing.unisannio.it/icnc2002/CP21Turbulent_Combustion-Deflagrations_Jets_&_Fires.pdf",
  note  = "Extended abstract"
}
@Unpublished{ep1,
  title = 	"An Inherently-Parallel Method for Solving Discretized Diffusion Equations",
  author = "Bradley R. Eccleston and Todd S. Palmer",
  institution = "Department of Nuclear Engineering, Oregon State University",
  url = "http://www.physics.orst.edu/\~{ }bertrand/stuff/Year_Two_Report.pdf",
  note = "Funded under the ASCI Level III: Computational Transport Issues for Large-Scale Parallel Simulations",
  year = 1999
}
@inproceedings{teo2007scalable,
  title={A scalable modular convex solver for regularized risk minimization},
  author={Teo, C.H. and Smola, A. and Vishwanathan, SVN and Le, Q.V.},
  booktitle={Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining},
  pages={727--736},
  year={2007},
  organization={ACM}
}
@InProceedings{rm02,
  author = "Robert Malouf",
  year   = "2002",
  title  = "A comparison of algorithms for maximum entropy Parameter estimation",
  booktitle = "In Proceedings of the Sixth Conference on Natural Language Learning (CoNLL-2002)",
  pages  = "49-55",
  url    = "http://bulba.sdsu.edu/malouf/papers/conll02.pdf"
}
@Unpublished{hrv02,
  title = 	"Computing the Lambda Modes of a Nuclear Reactor with {SLEPc} and {PETSc}",
  author = "V. Hernandex and J. E. Roman and V. Vidal",
  note = "Submitted to CMMSE",
}
@Article{tmh2001,
  author =        "Manfred Gilli and Evis Kellezi and Giorgio Pauletto",
  journal =      "Journal of Economic Dynamics and Control",
  year = "2002",
  volume = "26",
  pages = "1499-1515",
  title  =  "Solving finite difference schemes arising in trivariate option pricing"
}
@INPROCEEDINGS{a2,
        AUTHOR = "C.J.Palansuriya and C-H.Lai and C.S.Ierotheou and K.A.Pericleous and D.E.Keyes",
        TITLE = "Comparison of three algorithms for nonlinear metal cutting problems",
        BOOKTITLE = "Proceedings of the 11th International Conference on
                     Domain Decomposition Methods",
        EDITOR = "C.-H. Lai et al.",
        PUBLISHER = "Domain Decomposition Press, Bergen",
        url        = "http://www.ddm.org/DD11/Palansuriya.ps.gz",
        YEAR = "1999"
}
@Unpublished{mmmdcmaa-web-page,
  title = 	 "{M}ulti-{M}odel {M}ulti-{D}omain {C}omputational {M}ethods in {A}erodynamics and {A}coustics {W}eb Page",
  url = 	 "http://www.cs.odu.edu/\~{ }keyes/nsf",
  author =      "David E. Keyes",
  Institution = "Old Dominion University",
}
@conference{liu2010parallelization,
  title={{Parallelization of Thermal Recovery Simulation Based on PETSc}},
  author={Liu, L. and Xue, W. and Shu, J. and Ma, L.},
  booktitle={International Symposium on Parallel and Distributed Processing with Applications},
  pages={528--535},
  year={2010},
  organization={IEEE}
}
@Unpublished{oil-reservoir-sim-web-page,
  title = 	 "{N}ew {G}eneration {F}ramework for {P}etroleum, {R}eservoir {S}imulation",
  url = 	"http://www.pe.utexas.edu/CPGE/new_generation",
  institution = "University of Texas at Austin and Argonne National Laboratory",
  key         = "University of Texas at Austin and Argonne National Laboratory",
}
@Article{tmh2001b,
  author =        "V. Thiagarajan and K. Milfeld and KT. Milfeld",
  journal =      "IEEE TRANSACTIONS ON MAGNETICS ",
  year = "2001",
  volume = "37",
  pages = "143--146",
  title  =  "Adapting EMAP3D to parallel processing"
}
@Article{Harbury98,
  author =        "HK Harbury and W Porod",
  journal =      "VLSI Design",
  year = "1998",
  volume = "6",
  pages = "47--51",
  title  =       "Parallel computation for electronic waves in quantum corrals"
}
@Article{Bludszuwei98,
  author =        "Mark Bludszuweit",
  journal =      "Journal of Lightwave Technology",
  year = "1998",
  volume = "16",
  number = "7",
  pages = "1336--42",
  title  =       "Mixed Finite Element Beam Propagation Method"
}
@Article{s1,
  author =        "J. L. Friedman and N. Stergioulas",
  journal =      "Astrophysics Journal",
  year = "1998",
  volume = "492",
  number = "301",
  pages = "",
  title  =       ""
}
@Article{s1a,
  author =        "S. M. Morsink and N. Stergioulas and S. Blattnig",
  journal =      "Astrophysics Journal",
  year = "1999",
  volume = "510",
  number = "854",
  pages = "",
  title  =       ""
}
@phdthesis{s2,
 Author      = "N. Stergioulas",
 TITLE       = "Ph. D. thesis",
 year        = 1996,
 INSTITUTION = "University of Wisconsin-Milwaukee",
}
@inproceedings{coral1,
   AUTHOR	= "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
   TITLE	= "Solutions of TEAM Problem \#13 Using Integral Equations
                   in a Sequential and Parallel Computing Environment",
   BOOKTITLE	= "Proceedings of the Miami TEAM Workshop",
   LOCATION     = "Florida International University, Department of Electrical
                   Engineering and Computing Science",
   MONTH        = Nov,
   YEAR		= 1993
   }
@inproceedings{coral2,
   AUTHOR	= "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
   TITLE	= "Solutions of TEAM Problems 13 and 20 Using a Volume
                   Integral Formulation",
   BOOKTITLE	= "Proceedings of Aix-les-Bains TEAM Workshop",
   MONTH        = Dec,
   YEAR		= 1994
   }
@inproceedings{coral3,
   AUTHOR	= "L. Kettunen and K. Forsman and D. Levine and W. Gropp",
   TITLE	= "Computational Electromagnetics and Parallel Dense
                   Matrix Computations",
   BOOKTITLE	= "Proceedings of the SIAM Parallel Processing for
                   Scientific Computing Conference",
   LOCATION     = "Florida International University, Department of Electrical
                   Engineering and Computing Science",
   YEAR		= 1995
   }
@InProceedings{mijalkovic,
   author = {Slobodan Mijalkovi\'{c}},
   title = {Evaluation of Multigrid as a Solver for Stress Analysis Problems
             in Semiconductor Process Simulation},
   booktitle = {Multigrid Methods VI: Proceedings of the Sixth European
                Multigrid Conference Held Gent, Belgium, September 27--30, 1999.},
   editor = {Erik Dick, Kris Riemslagh, Jan Vierendeels},
   OPTvolume = {14},
   OPTseries = {Lecture Notes in Computational Science and Engineering},
   year = 2000,
   publisher = {Springer},
   address = {Berlin},
   OPTpages = {179--184},
}
@Article{Bludszuwei98a,
  author =        "Mark Bludszuweit",
  journal =      "Journal of Lightwave Technology",
  year = "1998",
  volume = "16",
  number = "7",
  pages = "1336--42",
  title  =       "Mixed Finite Element Beam Propagation Method"
}
@Article{gilli-pauletto-1998,
  author =       "Manfred Gilli and Giorgio Pauletto",
  title =        "Parallel {K}rylov Methods for Econometric Model Simulation",
  journal = "Computational Economics",
  year = "2000",
  volume = "16",
  pages = "173--186"
}
% LiteralHTML:
% LiteralHTML:  <a name="packages"></a><H3><center>Software Packages that use or interface to PETSc</center></H3>
% LiteralHTML:
@Article{CollierDalcinCalo2013,
  title   = {{PetIGA}: High-Performance Isogeometric Analysis},
  author  = {Nathan Collier and Lisandro Dalcin and Victor M. Calo},
  journal = {arxiv},
  year    = {2013},
  number  = {1305.4452},
  note    = {\url{http://arxiv.org/abs/1305.4452}},
}
@Article{CollierDalcinVignalCortesCalo2016,
  title   = {PetIGA: A framework for high-performance isogeometric analysis},
  author  = {Lisandro Dalcin and Nathan Collier and Philippe Vignal and AMA C{\^o}rtes and Victor M. Calo},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  year    = {2016},
}
@Misc{petiga-web-page,
  author       = {N. Collier and L. Dalcin and V.M. Calo},
  title        = {{PetIGA} {W}eb page},
  url          = {https://bitbucket.org/dalcinl/petiga/},
  howpublished = {\url{https://bitbucket.org/dalcinl/petiga/}},
  year         = {2014}
}
@article{Logg07,
  author={Logg, Anders},
  title={Automating the Finite Element Method},
  journal={Archives of Computational Methods in Engineering},
  volume={14},
  number={2},
  pages={93-138},
  year={2007},
  doi={10.1007/s11831-007-9003-9},
  url={http://dx.doi.org/10.1007/s11831-007-9003-9},
  publisher={Kluwer Academic Publishers},
  issn={1134-3060},
  language={English}
}
@article{JezequelCouturierDenis12,
  author={Jezequel, Fabienne and Couturier, Rapha\"el and Denis, Christophe},
  title={Solving large sparse linear systems in a grid environment: the GREMLINS code versus the PETSc library},
  journal={The Journal of Supercomputing},
  volume={59},
  number={3},
  pages={1517-1532},
  year={2012},
  issn={0920-8542},
  doi={10.1007/s11227-011-0563-y},
  url={http://dx.doi.org/10.1007/s11227-011-0563-y},
  publisher={Springer US},
  keywords={Asynchronous iterations; Grid computing; Iterative method; Multisplitting method; Sparse linear solver},
  language={English}
}

@Unpublished{feap-web-page,
  title       = {FEAP: A Finite Element Analysis Program},
  url         = {http://www.ce.berkeley.edu/projects/feap/},
  author      = {FEAP Team},
  note        = {Uses PETSc linear solvers - iterative and direct}
}

@Unpublished{parpre-web-page,
  title       = "{ParPre} {W}eb {P}age",
  url        =	"http://www.cs.utk.edu/\~{ }eijkhout/parpre.html",
  Institution = "University of Tennessee",
  author      = "Victor Eijkhout",
  note = "This is no longer supported. A set of preconditioners built on PETSc"
}
@Unpublished{pism,
  title = 	"{PISM}: a Parallel Ice Sheet Model",
  author = "{PISM Team}",
  abstract = "We have developed a numerical model of ice sheets called PISM (a Parallel Ice Sheet Model).  The thickness, temperature, velocity and age of the ice are all simulated, as is the deformation of the earth underneath the ice.  New techniques for fast ice dynamics, earth deformation, and verification have are included.",
  note = "\url{http://www.pism-docs.org/}"
}
@Unpublished{oofem,
  title = 	"OOFEM - an object oriented finite element package",
  author = "Borek Patzak",
  url = "http://www.oofem.org"
}
@Unpublished{dks2openfvm,
  title = 	"OpenFVM - a finite volume based general purpose CFD solver",
  author = "Open source development",
  url = "http://openfvm.sourceforge.net/"
}
@Unpublished{sundar-2008w,
  title = "DENDRO: a parallel geometric multigrid library for trilinear finite elements on octree meshes",
  author = "H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros",
  institution = "University of Pennsylvania",
  url = "http://www.seas.upenn.edu/~csela/dendro/html/index.html"
}
@Unpublished{khatiwala07-software,
  title = "A computational framework for simulation of biogeochemical tracers in the ocean",
  author = "Khatiwala, S.",
  institution = "Columbia University",
  url = "http://www.ldeo.columbia.edu/\~{ }spk"
}
@INBOOK{JiaoLiMa99,
 author    = "Xiangmin Jiao and Xiang-Yang Li and Xiaosong Ma",
 chapter     = "SIFFEA:Scalable Integrated Framework for Finite Element Analysis",
 url       = "http://portal.acm.org/citation.cfm?id=646895.709725",
 title = "Lecture Notes in Computer Science",
 publisher = "Springer-Verlag",
 volume    = 1732,
 year      = 1999
}
@Article{crow1,
   author = {C. S. Crow IV},
   title  = "DistSolve: An Open Source Web Service for Solving Sparse Systems of Equations",
   journal = "Hopkins Undergraduate Research Journal",
   year    = 2003,
   url = "http://www.jhu.edu/hurj/issue2/09D%20Crow%20DistSolve.pdf"
}
@Unpublished{petsc-python,
  title = 	"PETSc for Python",
  author = "L. Dalcin and R. Paz and M. Storti",
  institution = "International Center for Computer Methods in Engineering",
  url = "http://www.cimec.org.ar/python",
  note = "Provides Python bindings for PETSc via SWIG"
}
@Unpublished{cfdship,
  title = 	"{CFDShip-Iowa}",
  author = "Pablo M. Carrica and Robert V. Wilson and Fred Stern",
  institution = "University of Iowa",
  url = "http://www.iihr.uiowa.edu/\~{ }cfdship/",
  note = "CFDShip-Iowa is a multiblock free surface flow solver that uses overset structured grids, designed for ship applications"
}
@Unpublished{bvw,
  title = 	"Multiflow",
  author = "Berend van Wachem",
  institution = "Mechanical Engineering - Chalmers University of Technology",
  url = "http://www.tfd.chalmers.se/\~{ }berend/page3.html",
  note = "MultiFlow is a  curvlinear, multiblock, multiprocessor flowsolver for multiphase flows."
}
@Unpublished{dks2,
  title = 	"FENA - A Finite Element Model for the North Atlantic",
  author = "Jens Schroeter",
  institution = "Alfred-Wegener-Institute for Polar and Marine Research",
  url = "http://www.awi-bremerhaven.de/Modelling/INVERSE/FENAdesc/FENAdesc.html"
}
@techreport{piwonski2010idea,
  title={The Idea and Concept of {Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in {3-D}},
  author={Piwonski, J. and Slawig, T.},
  year={2010},
  institution={Christian-Albrechts-Universit\"at zu Kiel},
  url={http://www.informatik.uni-kiel.de/uploads/tx_publication/tr_1016_01.pdf}
}
@Unpublished{metos3d-web,
  title={{Metos3D}: {A} Marine Ecosystem Toolkit for Optimization and Simulation in 3-D},
  author={Piwonski, J. and Slawig, T.},
  institution={Christian-Albrechts-Universit\"at zu Kiel},
  url={http://www.informatik.uni-kiel.de/en/algorithmic-optimal-control/software/metos3d/}
}
@Unpublished{magpar,
   author     = "W. Scholz",
  title = 	"Magpar: Parallel Micromagnetics Code",
  Institution = "Vienna University of Technology",
  url = 	"http://magnet.atp.tuwien.ac.at/scholz/magpar/"
}
@Misc{libMesh:sourceforge,
  author        = {},
  title         = {{libMesh}:a C++ framework for the numerical simulation of partial differential equations on serial and parallel platforms},
  note          = {[Online]},
  URL  = {http://libmesh.github.io}
}
@misc{moose-web-page,
  title = {Multiphysics {O}bject-{O}riented {S}imulation {E}nvironment ({MOOSE})},
  author={David Andrs and Cody Permann and Andrew Slaughter and Richard Martineau and Derek Gaston and John Peterson and Jason Miller},
  institution = {Idaho National Laboratory},
  howpublished = {\url{http://mooseframework.org}}
}
@article{gaston2009moose,
  title={MOOSE: {A} parallel computational framework for coupled systems of nonlinear equations},
  author={Gaston, D. and Newman, C. and Hansen, G. and Lebrun-Grandi{\'e}, D.},
  journal={Nuclear Engineering and Design},
  volume={239},
  number={10},
  pages={1768--1778},
  year={2009},
  publisher={Elsevier}
}
@article{tonks2012object,
  title={An object-oriented finite element framework for multiphysics phase field simulations},
  author={Tonks, M.R. and Gaston, D. and Millett, P.C. and Andrs, D. and Talbot, P.},
  journal={Computational Materials Science},
  volume={51},
  number={1},
  pages={20--29},
  year={2012},
  publisher={Elsevier}
}
@Misc{PyLithManual,
  author = {Brad Aagaard and Sue Kientz and Matthew G. Knepley and Surendra Somala and Leif Strand and Charles Williams},
  title  = {{PyLith} User Manual Version 2.0.0},
  year   = {2014},
  url    = {http://geodynamics.org/cig/software/github/pylith/v2.0.0/pylith-2.0.0_manual.pdf}
}
@Misc{pylith-web-page,
  author = {Brad Aagaard and Matthew G. Knepley and Charles Williams},
  title  = {{PyLith}},
  year   = {2012},
  url    = {http://geodynamics.org/cig/software/pylith/},
  howpublished = {\url{http://geodynamics.org/cig/software/pylith/}}
}
@Misc{GaleManual,
  author = {Walter Landry and Luke Hodkinson and Susan Kientz},
  title = {Gale User Manual Version 2.0.0},
  year = {2011},
  url = {http://geodynamics.org/cig/software/gale/gale.pdf}
}
@Unpublished{underworld,
  author = "Louis Moresi",
  title = 	"{UnderWorld}: A Geodynamics Modelling Code",
  Institution = "Monash University",
  url = 	"http://www.mcc.monash.edu/twiki/view/Codes"
}
@article{moresi2007computational,
  title={Computational approaches to studying non-linear dynamics of the crust and mantle},
  author={Moresi, L. and Quenette, S. and Lemiale, V. and Meriaux, C. and Appelbe, B. and M{\"u}hlhaus, H.B.},
  journal={Physics of the Earth and Planetary Interiors},
  volume={163},
  number={1-4},
  pages={69--82},
  year={2007},
  publisher={Elsevier}
}
@article{pitt2009chaste,
  title={Chaste: a test-driven approach to software development for biological modelling},
  author={Pitt-Francis, J. and Pathmanathan, P. and Bernabeu, M.O. and Bordas, R. and Cooper, J. and Fletcher, A.G. and Mirams, G.R. and Murray, P. and Osborne, J.M. and Walter, A. and others},
  journal={Computer Physics Communications},
  volume={180},
  number={12},
  pages={2452--2471},
  year={2009},
  publisher={Elsevier}
}
@misc{fenicsproject,
  title={{The FEniCS project}},
  author={Logg, A. and {\O}lgaard, K. and Rognes, M.E. and Wells, G.N. and Jansson, J. and Kirby, R.C. and Knepley, M.G. and Lindbo, D. and Skavhaug, O.},
  note={A continually updated technical report. \url{http://fenicsproject.org}},
  url={http://fenicsproject.org},
  year={2011}
}
@Unpublished{Snark,
  title = 	"Snark:  A suite of software for geoscientific applications and a philosophy of scientific software development",
  Institution = "Victorian Partnership for Advanced Computing",
  url = 	"http://vpac.org/Snark"
}
@Misc{imoose:sourceforge,
  author        = {Guido Arians and Thomas Bauer and Christian Kaehler and
                   Wolfgang Mai and Christoph Monzel and Dirk {van Riesen} and
                   Christoph Schlensok},
  title         = {Innovative Modern Object-Oriented Solving Environment - {iMOOSE}},
  note          = {[Online]},
  URL  = {http://imoose.sourceforge.net}
}
@Unpublished{FoSSI,
   author     = "Stephan Frickenhaus",
  title = 	"FoSSI: Family of Simplified Solver Interfaces, offers scalable access to MPI-parallel
                 solvers from CSR-matrix format frequently used in sequential/vector codes",
  Institution = "AWI-Bremerhaven, Germanny",
  url = 	"http://www.awi.de/en/research/scientific_computing/research_topics_of_scientific_computing/fossi/"
}
@Unpublished{fun3dweb,
   author = "Dinesh Kaushik",
  title = 	"PETSC-FUN3D Benchmark Page",
  Institution = "ODU/ANL",
  url = 	"http://www.mcs.anl.gov/petsc-fun3d",
  note = "CFD Benchmark of some solvers in PETSc"
}
@Unpublished{scirun,
   author = "SCIRun Development Team",
  title = 	"SCIRun",
  Institution = "University of Utah",
  url = 	"http://www.sci.utah.edu/stories/2001/jul_scirun120.html",
  note = "SCIRun now uses PETSc linear solvers"
}
@misc{prometheus,
   author = "Mark F. Adams",
  title = 	"Prometheus - A scalable unstructured finite element solver",
  Institution = "Berkeley",
  howpublished = "\url{http://www.cs.berkeley.edu/~madams/prometheus}",
  url  = {http://www.cs.berkeley.edu/\~{ }madams/prometheus}
}
@Unpublished{Illuminator,
   author = "Adam C. Powell, IV",
   title  = "Illuminator Distributed Visualization Library",
   url   = "http://lyre.mit.edu/\~{ }powell/Illuminator.html"
}
@unpublished{rheoplast,
title  = "RheoPlast Phase Field Multi-Physics Code",
author = "Adam Powell and David Dussault and Bo Zhou",
url    = "http://lyre.mit.edu/\~{ }powell/rheoplast.html"
}
@Misc{tao-web-page,
  title   = "{Toolkit for Advanced Optimization (TAO)} {W}eb Page",
  author  = "Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild and Steve Benson and Lois Curfman McInnes and Jorge Mor{\'e}",
  Institution = "Mathematics and Computer Science Division, Argonne National Laboratory",
  howpublished = {\url{http://www.mcs.anl.gov/tao}}
}
@TechReport{tao-user-ref,
  title   = "{Toolkit for Advanced Optimization (TAO) users manual}",
  author  = "Alp Dener and Adam Denchfield and Todd Munson and Jason Sarich and Stefan Wild and Steve Benson and Lois Curfman McInnes",
  Institution = "Argonne National Laboratory",
  Year   = 2019,
  Number = "ANL/MCS-TM-322 - Rev 3.12"
}
%  url    = "http://www.mcs.anl.gov/tao",

@Unpublished{MEFpp-web-page,
  title       = "{MEF++} {W}eb {P}age",
  url        =	"http://www.giref.ulaval.ca/ressources/projets/mefpp.html",
  Institution = "Groupe Interdisiplinaire de Recherche en Elements Finis",
  author      = "Eric Chamberland",
  note = "A finite element code for fluid dynamics, solid mechanics, thermal and multiphysics"
}
@Unpublished{tipetsc-web-page,
  title = 	"Ti-PETSc - an interface to PETSc from Titanium",
  Institution = "Berkeley",
  url = 	"http://www.nersc.gov/\~{ }yunhe/cs267/final/paper.pdf"
}
@Unpublished{ptatin-web-page,
  title  = {ptatin3d},
  author = {Jed Brown and Laetitia {Le Pourhiet} and Dave A. May and Patrick Sanan},
  url    = {https://bitbucket.org/jedbrown/ptatin3d},
  year   = {2018},
}
@misc{multiphase-web-page,
  Author = "Q. Zou",
  title = 	"Multiphase flow with {PETSc}",
  Institution = "LANL",
  howpublished = "\url{http://cnls-www.lanl.gov/~qzou}",
  url = {http://cnls-www.lanl.gov/\~{ }qzou},
  Lab = {LANL}
}
@misc{electromag-web-page,
  title = 	"{EMSolve Web} page",
  Institution = "LLNL",
  howpublished = "http://www.llnl.gov/casc/emsolve",
  url = {http://www.Llnl.gov/casc/emsolve},
  author = "Daniel {White et al.}",
  Lab = {LLNL}
}
@Unpublished{fe-software-web-page,
  Institution = "Kuleuven",
  title =  "Finite element software",
  url = 	"http://www.esat.kuleuven.ac.be/elen/research/software-development"
}
@Misc{petsc-web-page,
  author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune
            and Kris Buschelman and Lisandro Dalcin and Alp Dener and Victor Eijkhout and William~D. Gropp
            and Dmitry Karpeyev and Dinesh Kaushik and Matthew~G. Knepley and Dave~A. May and Lois Curfman McInnes
            and Richard Tran Mills and Todd Munson and Karl Rupp and Patrick Sanan
            and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang},
  title =  {{PETS}c {W}eb page},
  url =    {https://www.mcs.anl.gov/petsc},
  howpublished = {\url{https://www.mcs.anl.gov/petsc}},
  year = {2019}
}
@Unpublished{petsc-debian-package,
    author = "Adam C. Powell, IV",
    title  = "Debian package for PETSc",
    url   = "http://lyre.mit.edu/\~{ }powell/petsc.html"
}
@Unpublished{cactus,
    title  = "Cactus Website",
    url   = "http://www.cactuscode.org/",
    note = "Provides two interface to the PETSc solvers"
}
@Unpublished{PETSc-FEM,
   author = "Mario Storti and Norberto Nigro",
  title = 	"PETSc-FEM: A General Purpose, Parallel, Multi-Physics FEM Program",
  Institution = "Centro Internacional de Metodos Computacionales en Ingenieria (CIMEC)",
  url = 	"http://www.cimec.org.ar/petscfem"
}
@misc{fidap,
  title = 	"FIDAP 8.5",
  howpublished = "\url{http://www.fluent.com}",
  url          = {http://www.fluent.com},
  note = 	"Fluent's commercial finite element fluid code uses PETSc for parallel linear solves.",
  key = 	"FIDAP 8.5"
}
@Unpublished{slepc,
  author =       "Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and
                  Andr\'es Tom\'as and Vicente Hern\'andez and Vicent Vidal",
  title = 	"{SLEPc} Homepage",
  url = 	"http://slepc.upv.es/",
  note = 	"Scalable Library for Eigenvalue Problem Computations"
}
@techreport{slepc-users-manual,
  author = "Carmen Campos and Jos\'e E. Rom\'an and Eloy Romero and
           Andr\'es Tom\'as and Vicente Hern\'andez and Vicent Vidal",
  title = 	"{SLEPc} Users Manual",
  number    = "DISC-II/24/02",
  url = 	"http://slepc.upv.es/",
  note = 	"Scalable Library for Eigenvalue Problem Computations"
}
@misc{deal.II,
  title = 	"deal.II",
  howpublished = "\url{http://www.dealii.org}",
  url          = {http://www.dealii.org},
  note = 	"deal.II is a C++ library targeting adaptive finite elements and error estimation. It allows PETSc linear algebra and solvers to be used underneath.",
  key = 	"deal.II 5.0"
}
@article{bangerth2007deal,
  title={{deal.II---A general-purpose object-oriented finite element library}},
  author={Bangerth, W. and Hartmann, R. and Kanschat, G.},
  journal={ACM Transactions on Mathematical Software (TOMS)},
  volume={33},
  number={4},
  pages={24--es},
  issn={0098-3500},
  year={2007},
  publisher={ACM}
}
@misc{globalarrays,
   author = "Jarek {Nieplocha et al.}",
  title = 	"Global Arrays",
  Institution = "Pacific Northwest National Laboratories",
  howpublished = 	"\url{http://www.emsl.pnl.gov/docs/global}",
  url =	{http://www.emsl.pnl.gov/docs/global},
  note = "Global arrays can use PETSc linear solvers",
  Lab = {PNNL}
}
% LiteralHTML:
% LiteralHTML:  <a name="software"><H3><center>Software Engineering</center></H3>
% LiteralHTML:
@article{BrownKnepleySmith14,
  author  = {Jed Brown and Matthew G. Knepley and Barry Smith},
  title   = {Run-time extensibility and librarization of simulation software},
  journal = {IEEE Computing in Science and Engineering},
  month   = {Jan},
  volume  = {17},
  number  = {1},
  pages   = {38--45},
  doi     = {10.1109/MCSE.2014.95},
  year    = {2015}
}
@TechReport{ass2012,
  author = {Shrirang Abhyankar and Barry Smith and  Kerry Stevens},
  title  = {Preliminary implementation of Hybrid {MPI}/pthread programming model in {PETSc}},
  institution = {Argonne National Laboratory},
  type = "Preprint",
  year   = 2012,
  number = "ANL/MCS-P2011-0112"
}

@techreport{ClearyKnepley99,
  author      = {Andrew Cleary and Matthew G. Knepley},
  title       = {Solvers as Operators},
  institution = {Lawrence Livermore National Laboratory},
  type        = {Technical Report},
  number      = {UCRL-ID-135342},
  year        = {1999}
}

@techreport{smcabbkz2012,
  author = "Barry Smith and Lois Curfman McInnes and Emil Constantinescu and Mark Adams and
            Satish Balay and Jed Brown and Matthew Knepley and Hong Zhang",
  title = "{PETSc's} software strategy for the design space of composable extreme-scale solvers",
  institution = "Argonne National Laboratory",
  type = "Preprint",
  note = "{DOE} Exascale Research Conference, April 16-18, 2012, Portland, OR",
  year = 2012,
  number = "ANL/MCS-P2059-0312"
}

@inproceedings{mhwpmhs2009,
  author    = {R. T. Mills and  F. M. Hoffman and P. H. Worley and K. S. Pwerumalla and A. Mirin and G. E. Hammond and  B. Smith},
  title     = {Coping at the User-Level with Resource Limitations in the {Cray} Message Passing Toolkit {MPI} at Scale},
  booktitle = {Cray Users Group Conference},
  year      = {2009}
}
@inproceedings{msmhls2010,
  author    = {R. T. Mills and V. Sripathi and G. Mahinthakumar and G. Hammond and P. C. Lichtner and B. F. Smith},
  title     = {Engineering {PFLOTRAN} for Scalable Performance on {Cray} {XT} and {IBM} {BlueGene} Architectures},
  booktitle = {Proceedings of SciDAC 2010 Annual Meeting},
  year      = {2010}
}
@incollection{msk2013,
  author    = {Victor Minden and Barry F. Smith and Matthew G. Knepley},
  title     = {Preliminary Implementation of {PETSc} Using {GPUs}},
  booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
  series    = {Lecture Notes in Earth System Sciences},
  editor    = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
  url       = {http://dx.doi.org/10.1007/978-3-642-16405-7_7},
  publisher = {Springer Berlin Heidelberg},
  pages     = {131--140},
  year      = {2013},
  isbn      = {978-3-642-16404-0},
}
@incollection{KnepleyYuen13,
  author    = {Matthew G. Knepley and David A. Yuen},
  title     = {Why Scientists and Engineers need {GPU}s today},
  booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
  series    = {Lecture Notes in Earth System Sciences},
  editor    = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
  doi       = {10.1007/978-3-642-16405-7_1},
  url       = {http://dx.doi.org/10.1007/978-3-642-16405-7_1},
  publisher = {Springer Berlin Heidelberg},
  pages     = {131--140},
  year      = {2013},
  isbn      = {978-3-642-16404-0},
}
@incollection{KarpeevKnepleyBrune13,
  author    = {Dmitry A. Karpeev and Matthew G. Knepley and Peter R. Brune},
  title     = {Accurate Evaluation of Local Averages on {GPGPUs}},
  booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
  series    = {Lecture Notes in Earth System Sciences},
  editor    = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
  doi       = {10.1007/978-3-642-16405-7_30},
  url       = {http://dx.doi.org/10.1007/978-3-642-16405-7_30},
  publisher = {Springer Berlin Heidelberg},
  pages     = {487--501},
  year      = {2013},
  isbn      = {978-3-642-16404-0},
}
@incollection{ZhengEtAl13,
  title     = {{GPU} Implementation of Multigrid Solver for {S}tokes Equation with Strongly Variable Viscosity},
  author    = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
  booktitle = {GPU Solutions to Multi-scale Problems in Science and Engineering},
  series    = {Lecture Notes in Earth System Sciences},
  editor    = {David A. Yuen and Long Wang and Xuebin Chi and Lennart Johnsson and Wei Ge and Yaolin Shi},
  doi       = {10.1007/978-3-642-16405-7_21},
  url       = {http://dx.doi.org/10.1007/978-3-642-16405-7_21},
  publisher = {Springer Berlin Heidelberg},
  pages     = {321--333},
  year      = {2013},
  isbn      = {978-3-642-16404-0},
}
@article{ZhengEtAl13b,
  title     = {Implementation of a multigrid solver on {GPU} for {S}tokes equations with strongly variable viscosity based on {M}atlab and {CUDA}},
  author    = {Liang Zheng and Taras Gerya and Matthew G. Knepley and David A. Yuen and Huai Zhang and Yaolin Shi},
  journal   = {IJHPCA},
  volume    = {28},
  number    = {1},
  pages     = {50--60},
  doi       = {10.1177/1094342013478640},
  url       = {http://hpc.sagepub.com/content/early/2013/03/03/1094342013478640.abstract},
  note      = {\url{http://hpc.sagepub.com/content/early/2013/03/03/1094342013478640.abstract}},
  year      = {2013}
}
@inbook{s2011,
  author = "B. Smith",
  chapter = "PETSc, the Portable, Extensible Toolkit for Scientific computing",
  title = "Encyclopedia of Parallel Computing",
  bookeditor = "D. Padua",
  publisher = "Springer",
  year = "2011"
}
@article{AcostaMejia06,
  author  = {Carlos D. Acosta and Carlos E. Mej\'ia},
  title   = {Computaci\'on cient\'ifica en paralelo con interfaz MATLAB a PETSc},
  journal = {Lecturas Matem\'aticas},
  volume  = {27},
  year    = {2006},
  pages   = {213--224}
}


@InProceedings{QuenetteMoresiSunterAppelbe07,
  author    = {Steve Quenette and Louis Moresi and {P. D.} Sunter and Bill F. Appelbe},
  title     = {Explaining StGermain: An aspect oriented environment for building extensible computational mechanics modeling software},
  booktitle = {Parallel and Distributed Processing Symposium, IPDPS 2007},
  publisher = {IEEE},
  pages     = {1--8},
  yerar     = {2007},
}
@Article{dfm1,
   title = "Vectorized sparse matrix multiply for compressed row storage format",
   author = "E. F. D'Azevedo and M. R. Fahey and R. T. Mills",
   journal= "Lecture Notes in Computer Science",
   year   = "2005",
   pages="99--106",
   volume="3514",
   lab = "ORNL"
}
@InProceedings{LaniQuintinoKimpeDeconinckVandewallePoedts05,
  author =       "Andrea Lani and Tiago Quintino and Dries Kimpe and Herman Deconinck and Stefan Vandewalle and Stefaan Poedts",
  title =        "The COOLFluiD Framework: Design Solutions for High Performance Object Oriented Scientific Computing Software",
  booktitle =    "Computational Science  ICCS 2005: 5th International Conference",
  year =         "2005",
  note =         "Lecture Notes in Computer Science",
  volume =       "3514",
  publisher =    "Springer-Verlag GmbH"
}
@InProceedings{dalcin-paz-storti,
  author =       "L. Dalcin and R. Paz and M. Storti",
  title =        "Desarrollo de Aplicaciones Paralelas en Python",
  booktitle =    "Proceedings of *XIV Congress on Numerical Methods and its Applications (ENIEF). Bariloche, Argentina",
  year =         "2004"
}
@Article{mpi-python,
  author =       "L. Dalcin and R. Paz and M. Storti",
  title =        "MPI for Python",
  journal = "Journal of Parallel and Distributed Computing",
  year = "2005"
}
@Unpublished{hrv02a,
  title = 	"{SLEPc}: Scalable Library for Eigenvalue Problem Computations",
  author = "V. Hernandex and J. E. Roman and V. Vidal",
  note = "Submited to VecPar 2002",
  year = 2002
}
@article{knyazev2007block,
  title={Block Locally Optimal Preconditioned Eigenvalue Xolvers {(BLOPEX)} in {Hypre} and {PETSc}},
  author={Knyazev, A. V. and Argentati, M. E. and Lashuk, I. and Ovtchinnikov, E. E.},
  journal={SIAM Journal on Scientific Computing},
  volume={29},
  pages={2224-2239},
  url={http://dx.doi.org/10.1137/060661624},
  year={2007}
}

@mastersthesis{aarrestad-master,
  author = "Asbjorn Hoiland Aarrestad",
  title =  "Time Dependent Solution of the Schrodinger Equation for Parallel Computers",
  school = "University of Bergen",
  month = "August",
  year = "2003",
  url = "http://www.parallab.uib.no/projects/molecul/matrix/",
  note = {Implemented Runge-Kutta methods using PETSc}
}
@phdthesis{kaushik-phd,
  author = "D. K. Kaushik",
  title =  "Performance Modeling and Prediction for the Scalable
            Solution of Partial Differential Equations on Unstructured
            Grids",
  school = "Old Dominion University",
  month = "December",
  year = "2002",
  url = "http://www.mcs.anl.gov/\~{ }kaushik/Papers/thesis.ps"
}
@techreport{rb1,
  AUTHOR=   "Rickard Bergstrom",
  TITLE=    "Object Oriented Implementation of a General Finite Element Code",
  NUMBER=   "2002-13",
  INSTITUTION= "Chalmers Finite Element Center, Chalmers University of Technology",
  YEAR=      2002,
  url = "http://www.phi.chalmers.se/pub/preprints/pdf/phiprint-2002-13.pdf",
  note = "Discribes a finite element software package that uses PETSc for its solvers"
}
@InProceedings{dbl1,
  author =       "Enzo A. Dari and Gustavo C. Buscaglia and Adrian J. Lew",
  title =        "A Parallel General Purpose Finite Element System",
  booktitle =    "IX SIAM Conference on Parallel Processing for Scientific Computing",
  publisher =    "SIAM",
  year =         "1999",
  url = "http://cabmec1.cnea.gov.ar/papers/apgpfes.ps.gz",
  note = "Describes software that uses PETSc for its parallel linear solves"
}
@Article{p1,
   title = "Parallel Components for PDEs and Optimization: Some Issues and Experiences",
   author = "B. Norris and S. Balay and S. Benson and L. Freitag and P. Hovland and L. McInnes and B. Smith",
   journal= "Parallel Computing",
   year   = "2002",
   pages="1811--1831",
   volume="28 (12)"
}
@Article{Automatic-AD,
  AUTHOR=   "Paul Hovland and Boyana Norris and Barry Smith",
  TITLE=    "Making Automatic Differentiation Truly Automatic: Coupling {PETSc} with {ADIC}",
  YEAR=      2005,
  journal = "Future Generation Computer Systems",
  volume = 21,
  number = 8,
  pages = "1426--1438"
}
@techreport{remote-math,
   author= "Elizabeth Dolan and Paul Hovland and Jorge Mor\'e and Boyana Norris and Barry Smith",
   title=  "Remote Access to Mathematical Software",
   number= "ANL/MCS-P889-0601",
   institution="Mathematics and Computer Science Division, Argonne National Laboratory",
   month= "June",
   year = "2001",
   url = "http://icm.mcs.kent.edu/research/iamc01proceedings.html"
}
@INPROCEEDINGS{ gropp98,
 AUTHOR=    "William D. Gropp",
 TITLE=     "Exploiting Existing Software in Libraries: Successes, Failures, and Reasons Why",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
                Inter-operable Scientific and Engineering Computing",
 year      = 1999,
 pages     = "21-29"
}
@INPROCEEDINGS{knepleysarin99,
  author    = {Matthew Knepley and Vivek Sarin},
  title     = {Algorithm Development for Large Scale Computing},
  publisher = {SIAM},
  booktitle = {Proceedings of the SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing},
  note      = {\url{http://books.google.com/books?id=2Da5OcnjPSgC&lpg=PA58&ots=TJCK64BUeg&dq=Bill%20Gropp%20Science%20Engineering%20Object%20Oriented&pg=PA138#v=onepage&q&f=false}},
  year      = {1999}
}
@INBOOK{bgms00,
 author    = "S. Balay and W. D. Gropp and L. C. McInnes and B. F. Smith",
 chapter     = "Software for the Scalable Solution of {PDEs}",
 url       = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P834.ps.Z",
 title = "CRPC Handbook of Parallel Computing",
 editor    = "J. Dongarra and I. Foster and G. Fox and B. Gropp and K. Kennedy and L. Torczon and A. White",
 publisher = "Morgan Kaufmann Publishers",
 year      = 2002
}
@INPROCEEDINGS{ hovland_norris_smith98,
 AUTHOR=    "Paul Hovland and Boyana Norris and Lucas Roh and Barry Smith",
 TITLE=     "Developing a Derivative-Enhanced Object-Oriented Toolkit for Scientific Computations",
 PUBLISHER= "SIAM",
 BOOKTITLE= "Proceedings of the SIAM Workshop on Object Oriented Methods for
                Inter-operable Scientific and Engineering Computing",
 url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P731.ps.Z",
 note      = "also available as Argonne preprint ANL/MCS-P731-1098",
 year      = 1999,
 pages     = "129-137"
}
@InProceedings{efficient,
  author    = "Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
  title     = "Efficient Management of Parallelism in
               Object Oriented Numerical Software Libraries",
  booktitle = "Modern Software Tools in Scientific Computing",
  editor    = "E. Arge and A. M. Bruaset and H. P. Langtangen",
  publisher = "Birkhauser Press",
  pages     = "163--202",
  year      = 1997
}
%  url       = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P634.ps.Z"
@TechReport{petsc-user-ref,
  author = {Satish Balay and Shrirang Abhyankar and Mark~F. Adams and Jed Brown and Peter Brune
            and Kris Buschelman and Lisandro Dalcin and Alp Dener and Victor Eijkhout and William~D. Gropp
            and Dmitry Karpeyev and Dinesh Kaushik and Matthew~G. Knepley and Dave~A. May and Lois Curfman McInnes
            and Richard Tran Mills and Todd Munson and Karl Rupp and Patrick Sanan
            and Barry~F. Smith and Stefano Zampini and Hong Zhang and Hong Zhang},
  title  = {{PETS}c Users Manual},
  institution = {Argonne National Laboratory},
  year   = 2020,
  number = {ANL-95/11 - Revision 3.13}
}
%  url    = {http://www.mcs.anl.gov/petsc}
@TechReport{petsc-developers,
  author = {Scott Kruger and Patrick Sanan and Barry~F. Smith},
  title  = {{PETS}c Developers Guide},
  institution = {Argonne National Laboratory},
  number      = {ANL-18/18},
  year   = 2018,
  url    = {http://www.mcs.anl.gov/petsc}
}
@Unpublished{alice-memory-snooper,
  author = {Ibrahima Ba and Barry~F. Smith},
  title = {The {ALICE} Memory Snooper},
  year = 1999
}
@TechReport{petsc-user-ref-polish,
    Author = "Marcin Bojko and Piotr Krzyzanowski",
    Title  = "Rozwiazywanie ukladow rownan przy pomocy pakietu PETSc",
    Institution = "Instytut Matematyki, Stosowanej i Mechaniki, Uniwersytet Warszawski",
    Year   = 1998,
    note   = "An introduction to PETSc in Polish"
    }
@inproceedings{abghmn00,
   title = "Integrating Automatic Differentiation with Object-Oriented
            Toolkits for High-Performance Scientific Computing",
   author = "J. Abate and S. Benson and L. Grignon and P. Hovland and
             L. C. McInnes and B. Norris",
   url       = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P820.ps.Z",
   booktitle = "Automatic Differentiation of Algorithms: From Simulation to Optimization",
   editor = {George Corliss and Christ\`{e}le Faure and Andreas Griewank and Laurent Hasco\"{e}t and Uwe Naumann},
   publisher = "Springer",
   year = "2002"
}
@Unpublished{petsc-mpi-paper,
    Author = "Lois Curfman McInnes and Barry F. Smith",
    Title  = "{PETS}c 2.0: A Case Study of Using {MPI} to Develop Numerical
              Software Libraries",
    Note   = "Proceedings of the MPI Developers Conference, Notre Dame, IN",
    Month  = Jun,
    Year   = "1995"
}
@INPROCEEDINGS{miss-paper,
 AUTHOR=    "William D. Gropp and Barry F. Smith",
 TITLE=     "Scalable, Extensible, and Portable Numerical Libraries",
 PUBLISHER= "IEEE",
 YEAR=      "1994",
 BOOKTITLE= "Proceedings of the Scalable Parallel Libraries Conference",
 ADDRESS=   "Mississippi State University",
 pages=     "87--93",
 keyword=   "numerical libraries, scientific computing, parallel computing"
}
@INPROCEEDINGS{snes-paper,
 AUTHOR=    "William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
 TITLE=     "Scalable Libraries for Solving Systems of Nonlinear Equations
             and Unconstrained Minimization Problems",
 PUBLISHER= "IEEE",
 YEAR=      "1995",
 BOOKTITLE= "Proceedings of the Scalable Parallel Libraries Conference",
 ADDRESS=   "Mississippi State University",
 pages=     "60-67",
 keyword=   "nonlinear equations, optimization, superconductivity, parallel
             computing"
}
@article{dsneutral,
  author  = {Barry F. Smith and William D. Gropp},
  title   = {The Design of Data-structure-neutral Libraries for the Iterative Solution of Sparse Linear Systems},
  journal = {Scientific Programming},
  volume  = {5},
  pages   = {329--336},
  key     = {GroppSmith96 ! KSP design},
  year    = {1996}
}
@inproceedings{bgms98,
 author    = "Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F. Smith",
 title     = "A Microkernel Design for Component-based Parallel Numerical Software Systems",
 booktitle = "Proceedings of the SIAM Workshop on Object Oriented Methods for
              Inter-operable Scientific and Engineering Computing",
 publisher = "SIAM",
 pages     = "58-67",
 url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P727.ps.Z",
 year      = "1998"
}
@Article{hkm98,
  author    = "M. E. Hayder and D. E. Keyes and P. Mehrotra",
  title     = "A Comparison of the {PETSc} Library and {HPF} Implementations of
               an Archetypal {PDE} Computation",
  journal   = "Advances in Engineering Software",
  volume    = 29,
  pages     = "415-424",
  year      = 1998
}
@techreport{pdpta99,
 AUTHOR=    "L. A. Freitag and W. D. Gropp and P. D. Hovland and L. C. McInnes and B. F. Smith",
 TITLE=     "Infrastructure and Interfaces for Large-Scale Numerical Software",
 note        = "to appear in the Proceedings of the 1999 International Conference
               on Parallel and Distributed Processing Techniques and Applications,
               June 28 - July 1, 1999, Las Vegas, Nevada",
 institution =  "Mathematics and Computer Science Division, Argonne National Laboratory",
 url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P751.ps.Z",
 number      = "ANL/MCS-P751-0599",
 year      = 1999
}
@inproceedings{bbh:com,
   author    ="C. H. Bischof and H. M. B{\"u}cker and P. D. Hovland",
   title     ="{On Combining Computational Differentiation and
                Toolkits for Parallel Scientific Computing}",
   booktitle ="Euro-Par 2000 -- Parallel Processing,
               Proceedings of the 6th International Euro-Par
               Conference, Munich, Germany, August/September 2000",
   year      = 2000,
   editor    ="A. Bode and T. Ludwig and W. Karl and R. Wism{\"u}ller",
   volume    ="1900",
   series    ="Lecture Notes in Computer Science",
   pages     ="86--94",
   address   ="Berlin",
   publisher ="Springer",
   url   = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P797.ps.Z"
}

@inproceedings{overture00,
  author      = "K. R. Buschelman and W. D. Gropp and L. C. McInnes and B. F. Smith",
  title       = " {PETSc and Overture}: Lessons Learned Developing an Interface between Components",
  url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P858.ps.Z",
  booktitle   = "Proceedings of the International Federation for Information
                 Processing Working Conference on Software Architectures for Scientific
                 Computing, Kluwer",
  year        = "2000",
  pages       = "57--68"
}
@techreport{smith97,
  title = 	 "An Interface for Efficient Vector Scatters and Gathers on Parallel Machines",
  url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P701.ps.Z",
  number        = "ANL/MCS-P701",
  author =      "Barry F. Smith",
  Institution = "Mathematics and Computer Science Division, Argonne National Laboratory"
}
@Article{smith98,
  author =       "Barry Smith",
  title  =       "The Transition of Numerical Software: From Nuts-and-Bolts to Abstraction",
  journal =      "SIGNUM Newsletter",
  year =         "1998",
  url         = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P712.ps.Z"
}
@techreport{AD-PETSC-TM,
  title = "Using {ADIFOR} and {ADIC} to Provide a {J}acobian for the {SNES} Component of {PETSc}",
  author = "Christian Bischof and Paul Hovland and Po-Ting Wu",
  year = 1997,
  type = "Technical Memorandum",
  institution = "ANL",
  url  = "ftp://info.mcs.anl.gov/pub/tech_reports/reports/TM233.ps.Z",
  number = "ANL/MCS-TM-233"
  }
% LiteralHTML:
% LiteralHTML:  <a name="algorithm"><H3><center>Algorithm design and analysis</center></H3>
% LiteralHTML:
@phdthesis{KlotzThesis2019,
  author = {Thomas S. Klotz},
  title  = {Numerical Analysis of Nonlinear Boundary Integral Equations Arising in Molecular Biology},
  school = {Rice University},
  year   = {2019}
}
@article{KlotzBardhanKnepley2018,
  title   = {Efficient Evaluation of Ellipsoidal Harmonics for Potential Modeling},
  author  = {Thomas S. Klotz and Jaydeep Bardhan and Matthew G. Knepley},
  journal = {Communications in Applied Mathematics and Computational Science},
  note    = {In review},
  url     = {https://arxiv.org/abs/1708.06028},
  year    = {2018}
}
@misc{Brown2016,
  title  = {Threading Tradeoffs in Domain Decomposition},
  author = {Jed Brown},
  note   = {SIAM Parallel Processing Conference, To Thread or Not To Thread Minisymposium, \url{https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf}},
  url    = {https://www.cse.buffalo.edu/~knepley/presentations/SIAMPP2016_1.pdf},
  year   = {2016}
}
@article{ChangNakshatralaKnepleyJohnsson2017,
  title   = {A performance spectrum for parallel computational frameworks that solve {PDEs}},
  author  = {Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley and Lennart Johnsson},
  journal = {Concurency: Practice and Experience},
  volume  = {30},
  number  = {11},
  eprint  = {1705.03625},
  doi     = {10.1002/cpe.4401},
  year    = {2017}
}
@article{ChangFabienKnepleyMills2018,
  title   = {Comparative study of finite element methods using the Time-Accuracy-Size {(TAS)} spectrum analysis},
  author  = {Justin Chang and Maurice S. Fabien and Matthew G. Knepley and Richard T. Mills},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {40},
  number  = {6},
  pages   = {C779--C802},
  eprint  = {1802.07832},
  doi     = {10.1137/18M1172260},
  year    = {2018}
}
@article{JoshaghaniChangNakshatralaKnepley2019,
  title   = {Composable solvers for the four-field double porosity/permeability model},
  author  = {M. S. Joshaghani and Justin Chang and Kalyana B. Nakshatrala and Matthew G. Knepley},
  journal = {Journal of Computational Physics},
  volume  = {386},
  pages   = {428--466},
  doi     = {10.1016/j.jcp.2019.02.020},
  year    = {2019}
}
@inproceedings{BarralKnepleyLangePiggottGorman2016,
  title     = {Anisotropic mesh adaptation in {Firedrake} with {PETSc} {DMPlex}},
  author    = {Nicolas Barral and Matthew G. Knepley and Michael Lange and Matthew D. Piggott and Gerard J. Gorman},
  booktitle = {25th International Meshing Roundtable},
  editor    = {Steve Owen and Hang Si},
  month     = {September},
  address   = {Washington, DC},
  pages     = {1--5},
  url       = {http://imr.sandia.gov/papers/imr25/2026_imr25RN_Barral.pdf},
  year      = {2016}
}

@article{AdamsBrownKnepleySamtaney2016,
  title   = {Segmental Refinement: A Multigrid Technique for Data Locality},
  author  = {Mark F. Adams and Jed Brown and Matthew G. Knepley and Ravi Samtaney},
  journal = {SIAM Journal on Scientific Computing},
  url     = {http://epubs.siam.org/toc/sjoce3/38/4 },
  epub    = {http://arxiv.org/abs/1406.7808},
  volume  = {8},
  number  = {4},
  pages   = {C426--C440},
  doi     = {10.1137/140975127},
  year    = {2016}
}
@inproceedings{MaySananRuppKnepleySmith2016,
  title     = {Extreme-Scale Multigrid Components within {PETSc}},
  author    = {Dave A. May and Patrick Sanan and Karl Rupp and Matthew G. Knepley and Barry F. Smith},
  booktitle = {Proceedings of the {Platform for Advanced Scientific Computing Conference}},
  series    = {PASC '16},
  isbn      = {978-1-4503-4126-4},
  location  = {Lausanne, Switzerland},
  pages     = {5:1--5:12},
  articleno = {5},
  numpages  = {12},
  doi       = {10.1145/2929908.2929913},
  acmid     = {2929913},
  publisher = {ACM},
  address   = {New York, NY, USA},
  keywords  = {GPU, HPC, agglomeration, coarse-level solver, multigrid, parallel computing, preconditioning},
  year      = {2016}
}
@article{liu2015field,
  title   = {Field-Split Preconditioned Inexact Newton Algorithms},
  author  = {Lulu Liu and David E Keyes},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {37},
  number  = {3},
  pages   = {A1388--A1409},
  year    = {2015},
  publisher = {SIAM}
}
@article{LuJiaoMissirlis2014,
  title   = {A hybrid geometric+ algebraic multigrid method with semi-iterative smoothers},
  author  = {Cao Lu and Xiangmin Jiao and Nikolaos Missirlis},
  journal = {Numerical Linear Algebra with Applications},
  volume  = {21},
  number  = {2},
  pages   = {221--238},
  year    = {2014},
  publisher = {Wiley Online Library}
}
@article{BadiaMartinPrincipe2013,
  title   = {Enhanced balancing Neumann-Neumann preconditioning in computational fluid and solid mechanics},
  author  = {Santiago Badia and Alberto F. Mart\'in and Javier Principe},
  journal = {International Journal for Numerical Methods in Engineering},
  volume  = {96},
  number  = {4},
  pages   = {203--230},
  year    = {2013}
}
@article{MorganKnepleySananScott2016,
  title   = {A Stochastic Performance Model for Pipelined {Krylov} Methods},
  author  = {Hannah Morgan and Matthew G. Knepley and Patrick Sanan and L. Ridgway Scott},
  journal = {Concurrency and Computation: Practice and Experience},
  volume  = {28},
  pages   = {4532--4542},
  year    = {2016},
  url     = {http://arxiv.org/abs/1602.04873},
  doi     = {10.1002/cpe.3820}
}

@article{msz2013,
  title={Efficient Sparse Matrix-Matrix Products Using Colorings},
  author={M. McCourt and B. F. Smith and H. Zhang},
  journal={SIAM Journal on Matrix Analysis and Applications},
  year={2015},
  note={To appear}
}
@article{bassi2014agglomeration,
  title={Agglomeration-based physical frame d{G} discretizations: {A}n attempt to be mesh free},
  author={Bassi, Francesco and Botti, Lorenzo and Colombo, Alessandro},
  journal={Mathematical Models and Methods in Applied Sciences},
  volume={24},
  number={08},
  pages={1495--1539},
  year={2014},
  publisher={World Scientific}
}
@ARTICLE{JhuraniDemkowicz12,
   author = {{Jhurani}, C. and {Demkowicz}, L.},
    title = "{Multiscale modeling using goal-oriented adaptivity and numerical homogenization. Part II: Algorithms for the Moore-Penrose pseudoinverse}",
  journal = {Computer Methods in Applied Mechanics and Engineering},
   volume = 213,
    pages = {418-426},
     year = 2012,
    month = mar,
      doi = {10.1016/j.cma.2011.06.003},
   adsurl = {http://adsabs.harvard.edu/abs/2012CMAME.213..418J}
}
@article{YangCai11,
  author = {Yang, Haijian and Cai, Xiao-Chuan},
  title = {Parallel Two-Grid Semismooth Newton-Krylov-Schwarz Method for Nonlinear Complementarity Problems},
  journal = {J. Sci. Comput.},
  issue_date = {May       2011},
  volume = {47},
  number = {2},
  month = may,
  pages = {258--280},
  year = {2011},
  issn = {0885-7474},
  numpages = {23},
  url = {http://dx.doi.org/10.1007/s10915-010-9436-4},
  doi = {10.1007/s10915-010-9436-4},
  acmid = {1971246},
  publisher = {Plenum Press},
  address = {New York, NY, USA},
  keywords = {Complementarity problem, Grid sequencing, Parallel computing, Schwarz preconditioners, Semismooth Newton, Two-level methods},
}
@article{Rheinbach09,
  author={Rheinbach, Oliver},
  title={Parallel Iterative Substructuring in Structural Mechanics},
  journal={Archives of Computational Methods in Engineering},
  volume={16},
  number={4},
  pages={425-463},
  year={2009},
  issn={1134-3060},
  doi={10.1007/s11831-009-9035-4},
  url={http://dx.doi.org/10.1007/s11831-009-9035-4},
  publisher={Springer Netherlands},
  language={English}
}
@Article{KnepleyTerrel2013,
  author   = {Matthew G. Knepley and Andy R. Terrel},
  title    = {Finite Element Integration on {GPUs}},
  journal  = {{ACM} Transactions on Mathematical Software},
  volume   = {39},
  number   = {2},
  accepted = {17 April 2012},
  year     = {2013},
  abstract = {We present a novel finite element integration method for
              low order elements on GPUs. We achieve more than 100GF
              for element integration on first order discretizations of
              both the Laplacian and Elasticity operators on an NVIDIA
              GTX285, which has a nominal single precision peak flop
              rate of 1 TF/s and bandwidth of 159 GB/s, corresponding
              to a bandwidth limited peak of 40 GF/s.},
  url       = {http://arxiv.org/abs/1103.0066},
  note      = {no. 10, \url{http://arxiv.org/abs/1103.0066}}
}
@online{KnepleyRuppTerrel2016,
  title       = {Finite Element Integration with Quadrature on the GPU},
  author      = {Matthew G. Knepley and Karl Rupp and Andy R. Terrel},
  version     = {1},
  date        = {2016-07-14},
  eprinttype  = {arxiv},
  eprintclass = {cs.MS},
  eprint      = {1607.04245v1}
}
@article{KlawonnLanserRheinbach2014,
  title   = {Nonlinear {FETI-DP} and {BDDC} Methods},
  author  = {Axel Klawonn and Martin Lanser and Oliver Rheinbach},
  journal = {SIAM Journal on Scientific Computing},
  volume  = {36},
  number  = {2},
  pages   = {A737--A765},
  year    = {2014},
}

@techreport{pbmkbsxt2012,
  title = "Composing Scalable Nonlinear Algebraic Solvers",
  author = "Peter R. Brune and Matthew G. Knepley and Barry F. Smith and  Xuemin Tu",
  year = 2013,
  type = "Preprint",
  number = "ANL/MCS-P2010-0112",
  institution = "Argonne National Laboratory"
}
@article{BruneKnepleySmithTu15,
  title   = {Composing Scalable Nonlinear Algebraic Solvers},
  author  = {Peter R. Brune and Matthew G. Knepley and Barry F. Smith and Xuemin Tu},
  journal = {SIAM Review},
  volume  = {57},
  number  = {4},
  pages   = {535--565},
  note    = {\url{http://www.mcs.anl.gov/papers/P2010-0112.pdf}},
  url     = {http://www.mcs.anl.gov/papers/P2010-0112.pdf},
  doi     = {http://dx.doi.org/10.1137/130936725},
  year    = {2015},
}

@article{mszm2014,
  title = "Hierarchical {Krylov} and nested {Krylov} methods for extreme-scale computing",
  author = "Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills",
  volume = {40},
  pages  = {17--31},
  year   = {2014},
  journal = "Parallel Computing",
  url = "http://dx.doi.org/10.1016/j.parco.2013.10.001"
}

@techreport{mszm2012,
  title = "Hierarchical {Krylov} and Nested {Krylov} Methods for Extreme-Scale Computing",
  author = "Lois Curfman McInnes and Barry Smith and Hong Zhang and Richard Tran Mills",
  year = 2012,
  number = "ANL/MCS-P2097-0512",
  institution = "Argonne National Laboratory"
}


@inproceedings{bkmms2012,
  author    = {Jed Brown and Matthew G. Knepley and David A. May and Lois C. McInnes and Barry F. Smith},
  title     = {Composable linear solvers for multiphysics},
  booktitle = {Proceeedings of the 11th {International Symposium on Parallel and Distributed Computing} ({ISPDC} 2012)},
  year      = {2012},
  doi       = {10.1109/ISPDC.2012.16},
  publisher = {IEEE Computer Society},
  pages     = {55--62},
}

@article{BourdinBucurOudet2009,
  author  = {Blaise Bourdin and D. Bucur and E. Oudet},
  title   = {Optimal Partitions for Eigenvalues},
  journal = {SIAM J. Sci. Comput.},
  volume  = {31},
  number  = {6},
  pages   = {4100--4114},
  year    = {2009}
}

@inbook{KimnBourdin2007,
  author    = {J.-H. Kimn and Blaise Bourdin},
  title     = {Numerical implementation of overlapping balancing domain decomposition methods on unstructured meshes},
  editor    = {O. B. Widlund and D. E. Keyes},
  booktitle = {Domain Decomposition Methods in Science and Engineering XVI},
  series    = {Lecture Notes in Computational Science and Engineering},
  number    = {55},
  publisher = {Springer-Verlag},
  pages     = {309--315},
  url       = "http://www.cims.nyu.edu/dd16/proceedings/kimn_bourdin_mini_6.pdf",
  year      = {2007}
}
@Article{bjm2005,
  author =   {AH Baker and ER Jessup and T Manteuffel},
  title =   {A Technique for Accelerating the Convergence of Restarted GMRES},
  journal =   {SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS},
  year =   {2005}
}
@unpublished{Sundar-2008a,
  author =   {R.S. Sampath and G. Biros},
  title =   {A parallel geometric multigrid method for finite elements on octree meshes},
  URL = {http://www.seas.upenn.edu/\~{ }rahulss}
}
@Article{Sundar-2008,
  author =   {H. Sundar and R.S. Sampath and G. Biros},
  title =   {Bottom-up construction and 2:1 balance refinement of linear octrees in parallel},
  journal =   {SIAM Journal on Scientific Computing},
  year =   {2008},
  URL = {http://www.seas.upenn.edu/\~{ }rahulss}
}
@InProceedings{Sundar-2007,
  author =   {H. Sundar and R.S. Sampath and S.S. Adavani and C. Davatzikos and G. Biros},
  title =   {Low-constant parallel algorithms for finite element simulations using linear octrees},
  booktitle =   {SC'07: ACM/IEEE Conference on Supercomputing},
  year =   {2007},
  URL = {http://www.seas.upenn.edu/\~{ }rahulss}
}
@InProceedings{Adams-98a,
  author =   {Adams, Mark ~F.},
  title =   {A Parallel Maximal Independent Set Algorithm},
  booktitle =   {Proceedings 5th copper mountain conference on iterative methods},
  year =   {1998}
}
@article{akcelik2005ddd,
  title={{Dynamic data-driven inversion for terascale simulations: real-time identification of airborne contaminants}},
  author={Ak\c{c}elik, V. and Biros, G. and Draganescu, A. and Hill, J. and Ghattas, O. and van Bloemen Waanders, B.},
  journal={Proceedings of the 2005 ACM/IEEE conference on Supercomputing},
  year={2005},
  publisher={IEEE Computer Society Washington, DC, USA}
}
@InBook{Akcelik-2006,
  author = {V. Akcelik and G. Biros and Omar Ghattas and J. Hill and David Keyes and B. van Bloemen Waanders},
  bookeditor = {M. Heroux and P. Raghaven and H. Simon},
  title = {Frontiers of Parallel Computing},
  chapter= {Parallel algorithms for {PDE}-constrained optimization},
  publisher = {SIAM},
  year = {2006}
}
@Article{dt,
  author =       "Matthew F. Dixon  and C. J. Kenneth Tan",
  title  =       "Using Distributed Computers to Deterministically Approximate Higher Dimensional Convection Diffusion Equations",
  journal =      "The Journal of Supercomputing",
  year =         "2004",
  pages = "235--253",
  volume = 28,
  url         = "http://www.springerlink.com/(nekina45nmdgrib5izizn3ip)/app/home/contribution.asp?referrer=parent&backto=issue,8,8;journal,20,73;linkingpublicationresults,1:100302,1"
}
@phdthesis{hwang2004,
   author = {Feng-Nan Hwang},
   title  = "Some Parallel Linear and Nonlinear {Schwarz} Methods with Applications in Computational Fluid Dynamics",
   school = {University of Colorado at Boulder},
   year   = 2004
}
@phdthesis{baker,
   author = {{A. H.} Baker},
   title  = "On improving the performance of the linear solver restarted {GMRES}",
   school = {University of Colorado at Boulder},
   year   = 2003
}
@techreport{KlawonnRheinbach601,
   author    ="Axel Klawonn and Oliver Rheinbach",
   title     ={A Parallel Implementation of Dual-Primal FETI-DP Methods for Three Dimensional Linear Elasticity
               Using a Transformation of Basis},
   institution ={Universit\"at Duisburg-Essen},
   year    = 2005,
   type    ="Technical Report",
   number  ="SM-E-601"
}
@techreport{KlawonnRheinbach609,
   author    ="Axel Klawonn and Oliver Rheinbach",
   title     ={Inexact FETI-DP Methods},
   institution ={Universit\"at Duisburg-Essen},
   year    = 2005,
   type    ="Technical Report",
   number  ="SM-E-609"
}
@techreport{KlawonnRheinbach607,
   author    ="Axel Klawonn and Oliver Rheinbach",
   title     ={Robust FETI-DP Methods for Heterogeneous Three Dimensional Elasticity Problems},
   institution ={Universit\"at Duisburg-Essen},
   year    = 2005,
   type    ="Technical Report",
   number  ="SM-E-607"
}
@Article{kul-natraj-pbp,
  author = {Kshitij Kulshreshtha and Neela Nataraj and Michael Jung},
  title = {Performance of a parallel mixed finite element implementation for fourth order clamped anisotropic
          plate bending problems in distributed memory environments},
  journal = {Applied Mathematics and Computation},
  volume = {155},
  year = {2004},
  number = 3,
  pages = {753--777}
}


@ARTICLE{Bramkamp2006UEJ,
       author = "F. D. Bramkamp and H. M. B{\"u}cker and A. Rasch",
       title = "Using Exact {J}acobians in an Implicit {N}ewton-{K}rylov Method",
       journal = "Computers \& Fluids",
       volume = "35",
       number = "10",
       pages = "1063--1073",
       doi = "10.1016/j.compfluid.2005.10.003 <http://dx.doi.org/10.1016/j.compfluid.2005.10.003>",
       abstract = "In an implicit Newton-Krylov method for inviscid, compressible fluid flow, the
         derivation of the analytic flux Jacobian can become quite complicated depending on the complexity of
         the numerical flux calculation. Practically, the derivation of the exact Jacobian by hand is an
         unrealistic option because of the enormous man-hour investment needed. In this work, automatic
         differentiation is used to evaluate the exact Jacobian of upwind schemes implemented in the flow
         solver QUADFLOW. We compare the use of exact Jacobians and Jacobians numerically approximated by
         first-order forward differences. For a two-dimensional airfoil under three different flight
         conditions (quasi-incompressible flow, compressible subsonic flow, and transonic flow), we show that
         the robustness and performance of the present finite volume scheme is significantly improved by
         using exact Jacobians.",
       year = "2006",
}

@Article{shahbazi1,
  author = {Khosro Shahbazi},
  title = {An explicit expression for the penalty parameter of the interior penalty method},
  journal = {Journal of Computational Physics},
  volume = {205},
  year = {2005},
  pages = {401--407}
}
@techreport{kk,
  title = "A Parallel Lanczos Algorithm for Eigensystem Calculation",
  author = "Hans-Peter Kersken and Uwe Kuster",
  year = 1999,
  institution = "University of Stuttgart",
  url  = "http://elib.uni-stuttgart.de/opus/volltexte/1999/310/pdf/310.pdf",
  number = "310"
  }
@Article{miha-mija,
  author = {M. D. Mihajlovi and S. Mijalkovi},
  title = {A component decomposition preconditioning for 3D stress analysis problems},
  journal = {Numerical Linear Algebra with Applications},
  volume = {9},
  year = {2002},
  pages = {567--583},
  url = {http://www3.interscience.wiley.com/cgi-bin/abstract/98516459/ABSTRACT}
}
@Article{bjm,
  author = "M Benzi and W Joubert and G Mateescu",
  journal = "Electronic Transactions on Numerical Analysis",
  year = "1999",
  volume = "8",
  pages = "88--114",
  title  =  "Numerical experiments with parallel orderings for {ILU} preconditioners",
  url = "http://scholar.google.com/url?sa=U&q=http://emis.bibl.cwi.nl/journals/ETNA/vol.8.1999/pp88-114.dir/pp88-114.ps"
}
@phdthesis{hyde,
   author = {EMK Hyde},
   title  = "Fast, High-Order Methods for Scattering by Inhomogeneous Media",
   school = {Caltech},
   year   = 2003,
   url = "http://www.acm.caltech.edu/\~{ }bruno/02hyde_thesis_print.pdf"
}
@Article{km2003,
  author = "A. Keese and H. G. Matthies",
  journal = "Proceedings in Applied Mathematics and Mechanics",
  year = "2003",
  volume = "2",
  pages = "485--486",
  title  =  "Parallel Solution of Stochastic PDEs",
  url = "http://www3.interscience.wiley.com/cgi-bin/abstract/104087421/ABSTRACT"
}
@Article{whszss,
  author = "Joachim Weickert and Josef Heers and Christoph Schnorr and Karel J. Zuiderveld and Otmar Scherzer and H. Siegfried Stiehl",
  journal = "Real Time Imaging",
  year = "2001",
  volume = "7",
  pages = "31--45",
  title  =  "Fast parallel algorithms for a broad class of nonlinear variational diffusion approaches",
  url = "http://www.mia.uni-saarland.de/weickert/Papers/TR_5_99.ps.gz"
}
@techreport{baker1,
  title = "An Efficient Block Variant of GMRES",
  author = "A. H. Baker and J. M. Dennis and E. R. Jessup",
  year = 2003,
  type = "Technical Report",
  institution = "University of Colorado, Boulder",
  url  = "http://www.scd.ucar.edu/css/staff/dennis/papers/block.pdf",
  number = "CU-CS-957-03"
  }
@INPROCEEDINGS{mc2003,
        AUTHOR = "Leszek Marcinkowski and Xiao-Chuan Cai",
        TITLE = "Parallel Performance of Some Two-Level {ASPIN} Algorithms",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "639--646",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@INPROCEEDINGS{kt2003,
        AUTHOR = "Deepak V. Kulkarni and Daniel A. Tortorelli",
        TITLE = "A Domain Decomposition Based Two-Level Newton Scheme for Nonlinear Problems",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "615--622",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@INPROCEEDINGS{krw2003,
        AUTHOR = "Axel Klawonn and Oliver Rheinbach and Olof B. Widlund",
        TITLE = "Some Computational Results for Dual-Primal FETI Methods for Elliptic Problems in 3D",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "361--368",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@INPROCEEDINGS{hc2003,
        AUTHOR = "Feng-Nan Hwang and Xiao-Chuan Cai",
        TITLE = "Improving Robustness and Parallel Scalability of {Newton's} Method Through Nonlinear Preconditioning",
        BOOKTITLE = "Proceedings of the 15th International Conference on
                     Domain Decomposition Methods",
        PAGES = "201--208",
        PUBLISHER = "Springer,  Lecture Notes in Computational Science and Engineering (LNCSE).",
        NOTE = "",
        URL = "http://www.ddm.org/DD15/proceedings-dd15.html",
        YEAR = "2003"
}
@INPROCEEDINGS{g2003,
        AUTHOR = "P. Goldfeld",
        TITLE = "Balancing {Neumann-Neumann} for (In)Compressible Linear Elasticity and (Generalized) {Stokes} and Parallel Implementation",
        BOOKTITLE = "Proceedings of the 14th International Conference on
                     Domain Decomposition Methods",
        PAGES = "209--216",
        EDITOR = "I. Herrera and D. Keyes and O. Widlund and R. Yates",
        PUBLISHER = "National Autonomous University of Mexico (UNAM)",
        NOTE = "",
        URL = "http://www.ddm.org/DD14",
        YEAR = "2003"
}
@INPROCEEDINGS{dhv2003,
        AUTHOR = "Zdenek Dostal and David Horak and Oldrich Vlach",
        TITLE = "Toward scalable FETI algorithm for variational inequalities with applications to composites",
        BOOKTITLE = "Proceedings of the 14th International Conference on
                     Domain Decomposition Methods",
        PAGES = "395--401",
        EDITOR = "I. Herrera and D. Keyes and O. Widlund and R. Yates",
        PUBLISHER = "National Autonomous University of Mexico (UNAM)",
        NOTE = "",
        URL = "http://www.ddm.org/DD14",
        YEAR = "2003"
}
@INPROCEEDINGS{dhsv2002,
        AUTHOR = "Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak",
        TITLE = "Scalabilities of FETI for variational inequalities and contact shape optimization",
        BOOKTITLE = "Proceedings of the 13th International Conference on
                     Domain Decomposition Methods",
        PAGES = "359--367",
        EDITOR = "N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov",
        PUBLISHER = "CIMNE,  Barcelona, Spain",
        NOTE = "",
        URL = "http://www.ddm.org/DD13",
        YEAR = "2002"
}
@INPROCEEDINGS{cky2002,
        AUTHOR = "Xiao-Chuan Cai and David E. Keyes and David P. Young",
        TITLE = "A Nonlinear Additive Schwarz Preconditioned Inexact Newton Method for Shocked Duct Flows",
        BOOKTITLE = "Proceedings of the 13th International Conference on
                     Domain Decomposition Methods",
        PAGES = "343--350",
        EDITOR = "N. Debit and M.Garbey and R. Hoppe and J. Periaux and D. Keyes and Y. Kuznetsov",
        PUBLISHER = "CIMNE,  Barcelona, Spain",
        NOTE = "",
        URL = "http://www.ddm.org/DD13",
        YEAR = "2002"
}
@CONFERENCE{li-etal:03,
  AUTHOR      = {Li, Z. and Lanteri S. and Saad, Y.},
  TITLE       = {Multiplicative-additive preconditioning combination
                  for general sparse linear systems},
  BOOKTITLE   = {2003 International Conference on Preconditioning
                  Techniques for Large Sparse Matrix Problems in
                  Scientific and Industrial Applications},
  ADDRESS     = {Napa, California, USA},
  DATE        = {october 27-29},
  YEAR        = {2003}
}
@article{bashir2008hessian,
  title={Hessian-based model reduction for large-scale systems with initial-condition inputs},
  author={Bashir, O. and Willcox, K. and Ghattas, O. and van Bloemen Waanders, B. and Hill, J.},
  journal={International journal for numerical methods in engineering},
  volume={73},
  number={6},
  pages={844--868},
  year={2008},
  publisher={Wiley Online Library}
}
@article{bashir2007hessian,
  title={Hessian-Based Model Reduction for Large-Scale Data Assimilation Problems},
  author={Bashir, O. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Willcox, K.},
  journal={Computational Science--ICCS 2007},
  pages={1010--1017},
  year={2007},
  publisher={Springer}
}
@article{akcelik2011fast,
  title={Fast algorithms for {B}ayesian uncertainty quantification in large-scale linear inverse problems based on low-rank partial {H}essian approximations},
  author={Ak\c{c}elik, V. and Flath, H.P. and Ghattas, O. and Hill, J. and van Bloemen Waanders, B. and Wilcox, L.},
  journal={SIAM Journal on Scientific Computing},
  volume={33},
  number={1},
  year={2011},
}
@inproceedings{ff2003,
  author="Abul K. M. Fahimuddin and Heike Fassbender",
  title="Model Reduction for Large Scale Applications in Microsystem Technology",
  booktitle="Proceedings of the 2004 SIAM Parallel Processing Conference",
  YEAR = "2003"
}
@inproceedings{d2b2004,
  author="Masoud Darbandi and Gerry E. Schneider and Seyed Mehi Bostandoost",
  title="Parallel Computation of a Fully Implicit Finite Volume Method Using Different Ordering Strategies",
  booktitle="Proceedings of AIAA Conference, Reno, Nevada",
  YEAR = "2004"
}
@inproceedings{d2v2005,
  author="Masoud Darbandi and Gerry E. Schneider and  Soheyl Vakili",
  title="A Comparative Study of Preconditioned Methods for Solving Fully Coupled Fluid Flow Equations",
  booktitle="The 13th Annual Conference on Computational Fluid Dynamics",
  YEAR = "2005"
}
@inproceedings{dvs2006,
  author="Masoud Darbandi and  Soheyl Vakili and Gerry E. Schneider",
  title="The Employment of Algebraic Multigrid as a Preconditioner to Solve Fully Implicit Mixed Convection Equations",
  booktitle=" The 44th AIAA Aerospace Sciences Meeting and Exhibit",
  YEAR = "2006"
}
@Article{dsv2006,
  author =       "Masoud Darbandi and Gerry E. Schneider and Soheyl Vakili",
  title  =       "Using Different Preconditioned Krylov Subspace Methods to Solve Coupled Fluid Flow Equations",
  journal =      "Computational Fluid Dynamics",
  year =         "2006",
  volume = 15,
  number = 1
}
@Article{Lahaye03,
  author =       "Lahaye, D. and Vandewalle, S. and Hameyer, K.",
  title  =       "An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems",
  journal =      "J. Comput. Appl. Math.",
  year =         "2004",
  pages = "267--275",
  volume = 168
}
@techreport{brmn,
  title = "Faster {PDE}-based Simulations Using Robust Composite Linear Solvers",
  author = "S. Bhowmick and P. Raghavan and L. McInnes and B. Norris",
  year = 2002,
  type = "Technical Report",
  institution = {ANL},
  number = "ANL/MCS-P993-0902",
  note="To appear in Future Generation Computer Systems"
  }
@inproceedings{mnbr,
  author="L. McInnes and B. Norris and S. Bhowmick and P. Raghavan",
  title="Adaptive Sparse Linear Solvers for Implicit {CFD} Using {Newton-Krylov} Algorithms",
  booktitle="Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics",
  YEAR = "2003",
}
@inproceedings{bmnr,
  author="S. Bhowmick and L. McInnes and B. Norris and P. Raghavan",
  title="The Role of Multi-Method Linear Solvers in {PDE}-based Simulations",
  booktitle="Proceedings of the 2003 International  Conference on Computational Science and its Applications,
             Lecture notes in Computer Science 2677",
  editor = "V. Kumar and M. L. Gavrilova and C. J. K. Tan and P. L'Ecuyer",
  pages = "828--839",
  YEAR = "2003",
}
@Article{ph03,
  author =       "M. Pernice and R. D. Hornung",
  title  =       "Newton-Krylov-FAC Methods for Problems Discretized on Locally Refined Grids",
  journal =      "Computing and Visualization in Science",
  year =         "2003",
  Lab = {LANL}
}

@article{Adams-02,
	Author = {Adams, M.~F. and Brezina, M. and Hu, J. J. and Tuminaro, R. S},
	Journal = {J. Comp. Phys.},
	Number = {2},
	Pages = {593-610},
	Title = {Parallel multigrid smoothing: polynomial versus {G}auss--{S}eidel},
	Volume = {188},
	Year = {2003}
}
@inproceedings{adams2001distributed,
  title={A distributed memory unstructured {G}auss-{S}eidel algorithm for multigrid smoothers},
  author={Adams, M.F.},
  booktitle={Supercomputing, ACM/IEEE 2001 Conference},
  pages={14--14},
  year={2001},
  organization={IEEE}
}
@PhdThesis{Els01,
  author =       {Ulrich Elsner},
  title =        {Static and Dynamic Graph Partitioning. A comparative study of existing algorithms},
  school =       {Technical University Chemnitz},
  year =         2002,
  publisher =    {Logos Verlag, Berlin},
  ISBN =         {3-89722-923-4},
  annote =       {Uses PETSc's high quality parallel algorithms to provide a
                  framework to compare different graph partitioning algorithms}
}
@techreport{ckk02,
  title = "Pseudo-Transient Continuation and Differential-Algebraic Equations",
  author = "Todd S. Coffey and C. T. Kelley and David E. Keyes",
  year = 2002,
  type = "Technical Report",
  institution = {ODU},
  url  = "http://www.math.odu.edu/\~{ }keyes",
  note="Submitted to the special issue of the SIAM Journal of Scientific Computing dedicated
        to papers from the 2002 Copper Mountain Conference on Iterative Methods"
  }
@Article{gpw2002,
  title = "Balancing Neumann-Neumann Preconditioners for Mixed Approximations of Heterogeneous
           Problems in Linear Elasticity",
  author = "Paulo Goldfeld and Luca F. Pavarino and Olof B. Widlund",
  year = 2003,
  pages = "283--324",
  volume = 95,
  url  = "http://www.cs.nyu.edu/csweb/Research/TechReports/TR2002-825/TR2002-825.pdf",
  journal="Numerische Mathematik"
  }
@Article{dh1,
  title = "Scalability and FETI based algorithm for large discretized variational inequalities",
  author = "Z Dostal and D Horak",
  year = 2003,
  pages = "347--357",
  volume = 61,
  url  = "http://portal.acm.org/citation.cfm?id=770222.770239",
  journal="Mathematics and Computers in Simulation"
  }
@inproceedings{dhsv1,
  author="Zdenek Dostal and David Horak and Jan Szweda and Vit Vondrak",
  url="http://cdcsp.univ-lyon1.fr/\~{ }dd13/DD13proc/Dostal.pdf",
  title="36 Scalabilities of FETI for Variational Inequalities and Contact Shape Optimization",
  booktitle="Proceedings of the 13th International Conference on Domain Decomposition Methods",
  editor=" N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. Kuznetsov"
}
@Article{Lahaye02,
  author =       "Domenico Lahaye and S. Vandewalle and K. Hameyer",
  title  =       "An Algebraic Multilevel Preconditioner for Field-Circuit Coupled Problems",
  journal =      "IEEEMAGN",
  year =         "2002",
  volume =       "38",
  number =       "2",
  pages =        "413-416"
}
@article{ckm01,
  author =  "X.-C. Cai and D. E. Keyes and L. Marcinkowski",
  url="http://www.cs.colorado.edu/homes/cai/public_html/papers/10page.ps",
  title="Nonlinear additive {Schwarz} preconditioners and applications in computational fluid dynamics",
  journal="International Journal of Numerical Methods in Fluid Mechanics",
  year = 2002,
  volume = 40,
  pages = "1463--1470"
}
@inproceedings{cky01,
  author="X.-C. Cai and D. E. Keyes and D. P. Young",
  url="http://www.cs.colorado.edu/homes/cai/public_html/papers/dd13_1d.ps",
  title="A nonlinear additive {Schwarz} preconditioned inexact {Newton} method for shocked duct flow",
  booktitle="Proceedings of the 13th International Conference on Domain Decomposition Methods",
  editor=" N. Debit and M. Garbey and R. Hoppe and J. Periaus and D. Keyes and Y. Kuznetsov",
  year=2002
}
@article{ck02,
  author="X.-C. Cai and D. E. Keyes",
  url="http://www.cs.colorado.edu/homes/cai/public_html/papers/aspin.ps",
  title="Nonlinearly preconditioned inexact {Newton} algorithms",
  journal="SIAM J. Sci. Comput.",
  year="2002",
  pages="183--200",
  volume="24"
}
@article{c04,
  author="Feng-Nan Hwang and X.-C. Cai",
  url="http://amath.colorado.edu/student/hwangf/papers/one-level-aspin.pdf",
  title="A parallel nonlinear additive {Schwarz} preconditioned inexact {Newton} algorithm for incompressible
       {Navier-Stokes} equations",
  journal="Journal of Computational Physics",
  year = 2005,
  volume = 204,
  pages = "666--691"
}
@article{hc06,
  author="Feng-Nan Hwang and X.-C. Cai",
  url="http://www.cs.colorado.edu/\~{ }cai/papers/aspin2_06.pdf",
  title="A Class of Parallel Two-Level Nonlinear {Schwarz} Preconditioned Inexact {Newton} Algorithms",
  journal="Computer Methods in Applied Mechanics and Engineering",
  year = 2006,
  volume = 196,
  pages = "1603--1611"
}
@InProceedings{Adams-01,
  author =   {Mark F. Adams},
  title =   {A Distributed Memory Unstructured {G}auss-{S}eidel Algorithm for Multigrid Smoothers},
  booktitle = {ACM/IEEE Proceedings of SC2001: High Performance Networking and Computing},
  address = {Denver, Colorado},
  month = {November},
  year = {2001}
}
@BOOK{1dl,
      AUTHOR="Domenico Lahaye",
      TITLE="Algebraic Multigrid for Two Dimensional Time-Harmonic Magnetic Field Computations",
      YEAR="2001",
      PUBLISHER="Katholieke Universiteit Leuven",
      NOTES="Thesis"
}

@article{Adams-00,
	Author = {Adams, M.~F.},
	Journal = {International Journal for Numerical Methods in Engineering},
	Number = {8},
	Pages = {1241-1262},
	Title = {Parallel Multigrid Solvers for 3{D} Unstructured Finite Element Problems in Large Deformation Elasticity and Plasticity},
	Volume = {48},
	Year = {2000}
}
@article{adams2002evaluation,
	Author = {Adams, M.~F.},
	Journal = {International Journal for Numerical Methods in Engineering},
	Number = {1},
	Pages = {519-534},
	Title = {Evaluation of Three Unstructured Multigrid Methods on 3{D} Finite Element Problems in Solid Mechanics},
	Volume = {55},
	Year = {2002}
}
@Article{Lahaye00,
  author =       "Domenico Lahaye and De Gersem, H. and Vandewalle, S. and Hameyer, K.",
  title  =       "Algebraic Multigrid for Complex Symmetric Systems",
  journal =      "IEEEMAGN",
  year =         "2000",
  volume =       "36",
  number =       "4",
  pages =        "1535--1538",
}

@InProceedings{Adams-99c,
  author =   {Mark F. Adams and J. Demmel},
  title =   {Parallel Multigrid Solver Algorithms and Implementations for 3{D} Unstructured Finite Element
                  Problems},
  booktitle = {Proceedings of SC99: High Performance Networking and Computing},
  address = {Portland, Oregon},
  month = {November},
  year = {1999}
}
@Article{chan95,
  author    = "T. Chan and B. Smith and J. Zou",
  title     = "Overlapping {S}chwarz Methods on Unstructured Meshes using Non-matching Coarse Grids",
  journal =   "Numer. Math.",
  year      = "1995",
  volume    = "73",
  pages     = "149--167"
}
@TechReport{Adams-CSD-98-993,
  pages =        "11",
  year =         "1998",
  type =         "Technical Report",
  number =       "CSD-98-993",
  institution =  "University of California, Berkeley",
  title =        "A Parallel Maximal Independent Set Algorithm",
  bibdate =      "March 11, 1998",
  author =       "Mark F. Adams and James Demmel",
  abstract =     "The parallel construction of maximal independent sets
                 is a useful building block for many algorithms in the
                 computational sciences, including graph coloring and
                 multigrid coarse grid creation on unstructured meshes.
                 We present an efficient asynchronous maximal
                 independent set algorithm for use on parallel
                 computers, for ``well partitioned'' graphs, that arise
                 from finite element (FE) models. For appropriately
                 partitioned bounded degree graphs, it is shown that the
                 running time of our algorithm under the P-RAM
                 computational model is of $O(1)$, which is an
                 improvement over the previous best P-RAM complexity for
                 this class of graphs. We present numerical experiments
                 on an IBM SP, that confirm our P-RAM complexity model
                 is indicative of the performance one can expect with
                 practical partitions on graphs from FE problems.",
  month =        mar # " 11,",
}
@TechReport{k676,
  year =         "1994",
  type =         "Technical Report",
  number =       "TR1994-676",
  institution =  "New York University",
  title =        "An Optimal Preconditioner for a Class of Saddle Point Problems with a Penalty Term",
  author =       "Axel Klawonn",
  url = 	"http://www.cs.nyu.edu/csweb/Research/TechReports/TR1994-676/TR1994-676.pdf"
}
@BOOK{ak1,
      AUTHOR="Axel Klawonn",
      TITLE="Preconditioners for Indefinite Problems",
      YEAR="1995",
      PUBLISHER="Westfalishen Wilhelms-Universitat Munster",
      url  = "http://www.cs.nyu.edu/csweb/Research/TechReports/TR1996-716/TR1996-716.pdf",
      NOTES="Thesis"
}

@TechReport{KnepleyKarpeev05,
  pages =        {41},
  year =         {2005},
  type =         {Technical Report},
  number =       {ANL/MCS-P1295-1005},
  institution =  {Argonne National Laboratory},
  title =        {Flexible Representation of Computational Meshes},
  author =       {Matthew G. Knepley and Dmitry A. Karpeev},
  abstract =     "",
  url =          {ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf},
  note =         {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1295.pdf}},
  month =        {October}
}

@TechReport{KnepleyKarpeev07A,
  pages =        "14",
  year =         "2007",
  type =         "Technical Report",
  number =       "ANL/MCS-P1455-0907",
  institution =  "Argonne National Laboratory",
  title =        "Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution",
  author =       "Matthew G. Knepley and Dmitry A. Karpeev",
  abstract =     "",
  url =          "ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf",
  note         = {\url{ftp://info.mcs.anl.gov/pub/tech_reports/reports/P1455.pdf}},
  month =        "February"
}

@article{KnepleyKarpeev09,
  author  = {Matthew G. Knepley and Dmitry A. Karpeev},
  title   = {Mesh Algorithms for {PDE} with {Sieve} {I}: {Mesh} Distribution},
  journal = {Scientific Programming},
  volume  = {17},
  number  = {3},
  pages   = {215--230},
  year    = {2009},
  doi     = {10.3233/SPR-2009-0249},
  url     = {http://arxiv.org/abs/0908.4427},
  note    = {\url{http://arxiv.org/abs/0908.4427}}
}
@article {biezuner2012computing,
   author = {Biezuner, Rodney and Brown, Jed and Ercole, Grey and Martins, Eder},
   affiliation = {Departamento de Matem\'atica—ICEx, Universidade Federal de Minas Gerais, Av. Ant\^onio Carlos 6627, Caixa Postal 702, 30161-970 Belo Horizonte, MG, Brazil},
   title = {Computing the First Eigenpair of the $p$-{L}aplacian via Inverse Iteration of Sublinear Supersolutions},
   journal = {Journal of Scientific Computing},
   publisher = {Springer Netherlands},
   issn = {0885-7474},
   keyword = {Mathematics and Statistics},
   pages = {180--201},
   volume = 52,
   issue = 1,
   year = 2012,
   url = {http://dx.doi.org/10.1007/s10915-011-9540-0},
   doi = {10.1007/s10915-011-9540-0}
}

% LiteralHTML:
% LiteralHTML:  <a name="books"><H3><center>Books</center></H3>
% LiteralHTML:
@book{Knepley2017,
  title     = {Computational Science I},
  author    = {Matthew G. Knepley},
  url       = {https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf},
  note      = {\url{https://www.cse.buffalo.edu/~knepley/classes/caam519/CSBook.pdf}},
  publisher = {PETSc},
  year      = {2017}
}
@article{verleyeuser,
  title={{User friendly permeability predicting software for technical textiles}},
  author={Verleye, B. and Morren, G. and Lomov, S.V. and Sol, H. and Verpoest, I. and Roose, D.},
  journal={status: published},
  issn={1560-6074},
  publisher={Hong Kong Polytechnic University, Hong Kong Institution of Textile and Apparel}
}
@BOOK{pacheco,
      AUTHOR="Peter Pacheco",
      TITLE="Parallel Programming with MPI",
      YEAR="1997",
      PUBLISHER="Morgan-Kaufmann",
      note="Devotes a couple of sections to PETSc"
}
@BOOK{1sbg,
      AUTHOR="Barry F. Smith and Petter Bj{\o}rstad and William D. Gropp",
      TITLE="Domain Decomposition: Parallel Multilevel Methods for Elliptic
             Partial Differential Equations",
      YEAR="1996",
      PUBLISHER="Cambridge University Press",
      url="http://www.mcs.anl.gov/~bsmith/ddbook.html"
}


@misc{petsc-fem:homepage,
   title = "{PETSc-FEM}: A General Purpose, Parallel, Multi-physics {FEM} Program",
   author = "M. Storti and N. Nigro and R. Paz and L. Dalcin and E. Lopez and L. Battaglia and G. Rodriguez and G. Filippini",
   howpublished = "\url{http://www.cimec.org.ar/twiki/bin/view/Cimec/PETScFEM}"
}
@misc{petsc4py-web-page,
  author = {Lisandro Dalcin},
  title  = {{PETSc} for {Python} -- {Python} bindings for {PETSc} libraries},
  howpublished = {\url{http://code.google.com/p/petsc4py/}},
  note   = {http://code.google.com/p/petsc4py/}
}

@article{libMeshPaper06,
  author = {B.~S.~Kirk and J.~W.~Peterson and R.~H.~Stogner and G.~F.~Carey},
  title = {{\texttt{libMesh}: A C++ Library for Parallel Adaptive Mesh
              Refinement/Coarsening Simulations}},
  journal = {Engineering with Computers},
  volume = {22},
  number = {3--4},
  pages = {237--254},
  year = {2006},
  note = {\url{http://dx.doi.org/10.1007/s00366-006-0049-3}}
}

@misc{sisiphus:homepage,
   title = "{SISIPHUS}: Scalable Ice-Sheet Solvers and Infrastructure for Petascale, High-Resolution, Unstructured Simulations",
   author = "T. {Tautges et al.}",
   howpublished = "\url{http://trac.mcs.anl.gov/projects/sisiphus/wiki}"
}

@misc{pflotran:homepage,
   title = "{PFLOTRAN} project",
   author = "Ben Andre and Gautam Bisht and Nathan Collier and Glenn Hammond and Satish Karra and Jitendra Kumar and Peter Lichtner and Richard Mills",
   howpublished = "\url{http://pflotran.org/}"
}

@misc{pism:homepage,
   title = "{PISM}: A Parallel Ice Sheet Model",
   author = "E. {Bueler et al.}",
   howpublished = "\url{http://pism-docs.org}"
}
@misc{dohp:homepage,
   title = "Dohp: Dual order $hp$-finite elements",
   author = "J. Brown",
   howpublished = "\url{http://dohp.org}"
}

@article{McCourtRognlienEtAl12,
 title = "Improving parallel scalability for edge plasma transport simulations with neutral gas species",
 author = "M. McCourt and T. D. Rognlien and L. C. McInnes and H. Zhang",
 journal = "Computational Science and Discovery",
 year = "2012",
 volume = "5",
 number = "014012",
 doi = "10.1088/1749-4699/5/1/014012",
 note = "Focus on 22nd International Conference on Numerical Simulations of Plasmas (ICNSP 2011)"
}

@misc{petclaw-github,
  title={Pet{C}law Software},
  author={Kyle T. Mandli and David I. Ketcheson and Amal Alghamdi and Aron Ahmadia},
  year={2011},
  howpublished={\url{https://github.com/pyclaw/pyclaw}}
}
@misc{pyclaw-web-page,
   author       = {Kyle T. Mandli and David I. Ketcheson and others},
   title        = {{PyClaw} software},
   howpublished = {\url{http://clawpack.github.io/doc/pyclaw/}},
   url          = {http://clawpack.github.io/doc/pyclaw/},
   year         = {2012}
}
@article{ketcheson2011highorder,
  title={High-order wave propagation algorithms for general hyperbolic systems},
  author={Ketcheson, David I. and Parsani, Matteo and LeVeque, Randall J.},
  year={2011},
  note={submitted}
}

@article{biros2005pln1,
  title={{Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE} constrained optimization. Part I: The {Krylov-Schur} solver}},
  author={Biros, G. and Ghattas, O.},
  journal={SIAM Journal on Scientific Computing},
  volume={27},
  number={2},
  pages={687--713},
  year={2005},
  publisher={Society for Industrial and Applied Mathematics Philadelphia, PA, USA}
}
@article{biros2005pln2,
  title={Parallel {Lagrange-Newton-Krylov-Schur} methods for {PDE}-constrained optimization. Part {II}: The {Lagrange Newton} solver, and its application to optimal control of steady viscous flows},
  author={Biros, G. and Ghattas, O.},
  journal={SIAM Journal on Scientific Computing},
  volume={27},
  number={2},
  pages={714--739},
  year={2005},
  publisher={Society for Industrial and Applied Mathematics Philadelphia, PA, USA}
}
@misc{issm:homepage,
  title={{I}ce {S}heet {S}ystem {M}odel},
  author={Eric Larour and Mathieu Morlighem and Helene Seroussi},
  year={2010},
  note={\href{http://issm.jpl.nasa.gov}{\url{issm.jpl.nasa.gov}}}
}
@article{morlighem2010spatial,
  title={Spatial patterns of basal drag inferred using control methods from a full-{S}tokes and simpler models for {P}ine {I}sland {G}lacier, {W}est {A}ntarctica},
  author={Morlighem, M. and Rignot, E. and Seroussi, H. and Larour, E. and Dhia, H.B. and Aubry, D.},
  journal={Geophysical Research Letters},
  volume={37},
  number={14},
  pages={L14502},
  year={2010},
  publisher={American Geophysical Union}
}
@article{Jardin2012plasmas,
  title={Multiple timescale calculations of sawteeth and other global macroscopic dynamics of tokamak plasmas},
  author={S. C. Jardin and N. Ferraro and J. Breslau and J. Chen},
  journal={Computational Science \& Discovery},
  volume={5},
  number={1},
  url   ="http://stacks.iop.org/1749-4699/5/014002",
  year={2012},
}

@article{cmz2016,
  title = {Analysis and Practical Use of Flexible {BiCGStab}},
  author = {Jie Chen and Lois Curfman McInnes and Hong Zhang},
  journal={Journal of Scientific Computing},
  publisher = {Springer},
  pages = {803--825},
  volume = {68},
  issue = {2},
  url = {http://link.springer.com/article/10.1007/s10915-015-0159-4},
  doi = {10.1007/s10915-015-0159-4},
  year = {2016},
  note={Also preprint ANL/MCS-P3039-0912}
}

@article{KnepleyBrownRuppSmith13,
  author   = {{Knepley}, M.~G. and {Brown}, J. and {Rupp}, K. and {Smith}, B.~F.},
  title    = {Achieving High Performance with Unified Residual Evaluation},
  journal  = {ArXiv e-prints},
  eprint   = {1309.1204},
  archivePrefix = "arXiv",
  primaryClass  = "cs.MS",
  keywords = {Computer Science - Mathematical Software, Computer Science - Computational Engineering, Finance, and Science},
  year     = 2013,
  month    = sep,
  adsurl   = {http://adsabs.harvard.edu/abs/2013arXiv1309.1204K},
  adsnote  = {Provided by the SAO/NASA Astrophysics Data System}
}

@book{FEniCSBook,
  title  = {Automated Solution of Differential Equations by the Finite Element Method: The FEniCS Book},
  series = {Lecture Notes in Computational Science and Engineering},
  volume = {84},
  editor = {Anders Logg, Kent-Andre Mardal, Garth Wells},
  publisher = {Springer},
  isbn   = {978-3-642-23098-1},
  year   = {2012}
}

@ARTICLE{DemidovAhnertRuppGottschling12,
  author = {{Demidov}, D. and {Ahnert}, K. and {Rupp}, K. and {Gottschling}, P.},
  title = "{Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries}",
  journal = {ArXiv e-prints},
  archivePrefix = "arXiv",
  eprint = {1212.6326},
  primaryClass = "cs.MS",
  keywords = {Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Computational Physics},
  year = 2012,
  month = dec,
  adsurl = {http://adsabs.harvard.edu/abs/2012arXiv1212.6326D},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@INPROCEEDINGS{ViennaCL,
 author={Rupp, K. and Rudolf, F. and Weinbub, J.},
 title={{ViennaCL - A High Level Linear Algebra Library for GPUs and Multi-Core CPUs}},
 booktitle={Intl.~Workshop on GPUs and Scientific Applications},
 year={2010},
 pages={51-56},
}
@article{KnepleyBrownMcInnesSmithRuppAdams2015,
  title  = {Exascale Computing without Threads},
  author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and Karl Rupp and Mark Adams},
  url    = {https://figshare.com/articles/Exascale_Computing_without_Threads-Barry_Smith_pdf/5824950},
  note   = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance},
  doi    = {10.6084/m9.figshare.5824950.v1},
  year   = {2015}
}
@article{KnepleyBrownMcInnesSmithRuppAdams2015b,
  title  = {Overview of the {PETSc} Library},
  author = {Matthew G. Knepley and Jed Brown and Lois Curfman McInnes and Barry Smith and Karl Rupp and Mark Adams},
  url    = {http://www.orau.gov/hpcor2015/whitepapers/Overview_of_the_PETSc_Library-Lois_McInnes.pdf},
  note   = {Whitepaper for the DOE High Performance Computing Operational Review (HPCOR) on Scientific Software Architecture for Portability and Performance},
  year   = {2015}
}
@inbook{BalayBrownKnepleyMcInnesSmith2015,
  author     = {Satish Balay and Jed Brown and Matthew G. Knepley and Lois McInnes and Barry Smith},
  bookeditor = {J. Carver},
  title      = {Software Engineering for Science},
  chapter    = {Providing Mixed Language and Legacy Support within a Library},
  publisher  = {Taylor \& Francis},
  year       = {2015}
}
@article{RuppBalayBrownKnepleyMcInnesSmith2015,
  title   = {On The Evolution Of User Support Topics in Computational Science and Engineering Software},
  author  = {Karl Rupp and Satish Balay and Jed Brown and Matthew G. Knepley and Lois Curfman McInnes and Barry F. Smith},
  note    = {Whitepaper for Computational Science \& Engineering Software Sustainability and Productivity Challenges},
  journal = {ArXiv e-prints},
  archivePrefix = {arXiv},
  eprint = {1510.01122},
  year   = {2015}
}

@inproceedings{knepley2013accurately,
  title={Accurately Citing Software and Algorithms Used in Publications},
  author={Knepley, Matthew G. and Brown, Jed and McInnes, Lois Curfman and Smith, Barry F.},
  year={2013},
  booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE), held at SC13},
  doi={http://files.figshare.com/1187013/paper.pdf}
}

@inproceedings{MillerEtAl2013,
  title={Package Management Practice Essential for Interoperability:  Lessons Learned and Strategies Developed for {FASTMath}},
  author={Mark C. Miller and Lori Diachin and Satish Balay and Lois Curfman McInnes and Barry Smith},
  year={2013},
  booktitle = {First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE), held at SC13},
  doi={10.6084/m9.figshare.789055}
}

@techreport{DudsonEtAl2012,
  title = {Improved Nonlinear Solvers in {BOUT++}},
  author = {Ben Dudson and Sean Farley and Lois Curfman McInnes},
  institution = {Argonne National Laboratory},
  number = {ANL/MCS-P3025-0812},
  year = 2012
}

@misc{Brown13,
  author = {J. Brown},
  title = {Scalable Repository Workflows},
  note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
  year = 2013
}

@misc{StarForest11,
  title  = {Star forests as a parallel communication model},
  author = {Jed Brown},
  url    = {https://jedbrown.org/files/StarForest.pdf},
  year   = {2011}
}

@misc{BrownKnepleySmith13,
  author = {J. Brown and M. Knepley and B. Smith},
  title = {Run-time Extensibility: Anything Less is Unsustainable},
  note = {whitepaper submitted to DOE Workshop on Software Productivity for Extreme-Scale Science, available via \url{http://www.orau.gov/swproductivity2014/papers.htm}},
  year = 2013
}

@article{JZhaoYLiWKLiu15,
  author   = "J. Zhao and Y. Li and W.K. Liu",
  title    = "Predicting band structure of 3{D} mechanical metamaterials with complex geometry via {XFEM}",
  journal  = "Computational Mechanics",
  year     = 2015,
  url = "http://link.springer.com/article/10.1007/s00466-015-1129-2"
}

@Article{alisic14,
  author =       {L. Alisic and J.F. Rudge and R.F. Katz and G. Wells and S. Rhebergen},
  title =        {Compaction around a rigid, circular inclusion in partially molten rock},
  journal =      {J. Geophys. Res.},
  year =         {2014},
  volume =       {119},
  number =       {7},
  pages =        {5903-5920},
  doi =          {10.1002/2013JB010906}
}

@Article{rhebergen14,
  author =       {S. Rhebergen and G. Wells and R.F. Katz and A. Wathen},
  title =        {Analysis of block preconditioners for models of coupled magma mantle dynamics},
  journal =      {SIAM J. Sci. Comp.},
  year =         {2014},
  volume =       {36},
  number =       {4},
  pages =        {1960-1977},
  doi =          {10.1137/130946678}
}

@Article{allwright14,
  author =       {J. Allwright and R.F. Katz},
  title =        {Pipe Poiseuille flow of viscously anisotropic, partially molten rock},
  journal =      {Geophys. J. Int.},
  year =         {2014},
  volume =       {199},
  number =       {3},
  pages =        {1608--1624},
  doi =          {10.1093/gji/ggu345}
}

@misc{Gropp10,
  author  = {William D. Gropp},
  title   = {Update on libraries for {B}lue {W}aters},
  address = {Bordeaux, France},
  year    = {2010},
  url     = {http://jointlab.ncsa.illinois.edu/events/workshop3/pdf/presentations/Gropp-Update-on-Libraries.pdf},
}

@article{SSM2016,
  author = {P. Sanan and S.M. Schnepp and D.A. May},
  title = {Pipelined, Flexible {Krylov} Subspace Methods},
  journal = {SIAM Journal on Scientific Computing},
  volume = {38},
  number = {5},
  pages = {C441-C470},
  year = {2016},
  doi = {10.1137/15M1049130},
}
@inproceedings{MayKnepley2017,
  title     = {{DMSwarm}: Particles in {PETSc}},
  author    = {Dave A May and Matthew G Knepley},
  booktitle = {EGU General Assembly Conference Abstracts},
  volume    = {19},
  pages     = {10133},
  year      = {2017}
}
@inproceedings{AdamsBrownKnepley2013,
    author       = {Mark F. Adams and Jed Brown and Matthew G. Knepley},
    title        = {Low-communication techniques for extreme-scale multilevel solvers},
    booktitle    = {Exascale Mathematics Workshop, Aug 21--22, Washington, DC},
    organization = {DOE Office of Advanced Scientific Computing Research},
    year         = {2013}
}
@article{BhallaGriffithKnepleyAdamsGuy2017,
  title   = {Scalable smoothing strategies for a geometric multigrid method for the immersed boundary equations},
  author  = {Amneet Pal Singh Bhalla and Boyce E. Griffith and Matthew G. Knepley and Mark F. Adams and Robert D. Guy},
  journal = {Advances in Computational Mathematics},
  eprint  = {1612.02208},
  note    = {In review},
  year    = {2017}
}
@article{zampini2016pcbddc,
  title={{PCBDDC}: a class of robust dual-primal methods in {PETSc}},
  author={Zampini, Stefano},
  journal={SIAM Journal on Scientific Computing},
  volume={38},
  number={5},
  pages={S282--S306},
  year={2016},
  publisher={SIAM}
}
@article{BergerVergiatWaisman2017,
  title   = {An overlapping Domain Decomposition preconditioning method for monolithic solution of shear bands},
  author  = {Luc Berger-Vergiat and Haim Waisman},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {318},
  pages   = {33--60},
  year    = {2017},
}
@article{AbhyankarMaldonadoSmithZhang2018,
  title   = {{PETSc} {DMNETWORK}: A Scalable Network Multiphysics Simulator},
  author  = {S. Abhyankar and D. A. Maldonado and B. Smith and H. Zhang},
  journal = {Submitted},
  volume  = {},
  pages   = {},
  year    = {2018},
}

@techreport{ZhangELLPACK2018,
 author = "Hong Zhang and Richard T. Mills and Karl Rupp and Barry F. Smith",
 title = "Vectorized Parallel Sparse Matrix-Vector Multiplication in {PETSc} Using {AVX-512}",
 number = "ANL/MCS-P9058-0418",
 institution = "Argonne National Laboratory",
 note = "submitted to the International Conference on Parallel Processing (ICPP) 2018",
 year = 2018
}

@misc{petsc-user-meetings:website,
  title ="{PETSc User Meetings}",
  key ="PETSc User Meetings",
  howpublished="\url{http://www.mcs.anl.gov/petsc/meetings}"
}

@article{flexible-bicgstab-chen16,
  title = {Analysis and Practical Use of Flexible {BiCGStab}},
  author = {J. Chen and L.C. McInnes and H. Zhang},
  journal = {Journal of Scientific Computing},
  volume = 68,
  number = 2,
  month = {July},
  year = 2016,
  pages = {803--825},
  DOI = {10.1007/s10915-015-0159-4}
}

@misc{petsc-extensibility2016,
  author = {M. Knepley and D. A. May and J. Brown and B. Smith},
  title = "{Extensibility in PETSc}",
  note = {SIAM News, available via \url{https://sinews.siam.org/Details-Page/extensibility-in-petsc}},
  year = 2016
}

@misc{error-estimation-whitepaper2017,
  author = {E. Constantinescu and O. Marin and T. Munson and B. Smith and H. Zhang},
  title = {End-to-end error estimation and control},
  note = {whitepaper for 2017 ASCR Applied Mathematics PI Meeting, accessible via \url{https://doi.org/10.6084/m9.figshare.5339866}},
  year = 2017
}

@misc{petsc-user-support15,
  title = {On the Evolution of User Support Topics in Computational Science and Engineering Software},
  author = {K. Rupp and S. Balay and J. Brown and M. Knepley and L. C. McInnes and B. Smith},
  note = {Workshop on CSE Software Sustainability and Productivity (CSESSP) Challenges, Oct 15-16, 2015},
  year = 2015
}

@inbook{petsc-mixed-language-support2016,
  title = {Numerical Library Support for High-Performance Mixed Language Applications and Legacy Code},
  author = {S. Balay and J. Brown and M. Knepley and L.C. McInnes and B. Smith},
  booktitle = {Software Engineering for Science},
  editors = {J. Carver et al.},
  publisher = {CRC Press},
  pages = {201--214},
  year = 2016
}
@inproceedings{konolige2018parallel,
  title={A Parallel Solver for Graph {L}aplacians},
  author={Tristan Konolige and Jed Brown},
  booktitle={Proceedings of the Platform for Advanced Scientific Computing (PASC)},
  doi={10.1145/3218176.3218227},
  note={Best Paper Award},
  archivePrefix={arXiv},
  eprint={1705.06266},
  year={2018}
}

@inproceedings{Werner-Kimn2019,
  title={Parallel implementation of AC optimal power flow and time-constrained optimal power flow using high-performance computing},
  author={Alex Werner and Kapil Duwadi and Nicholas Stegmeier and Timothy M. Hansen and Jung-Han Kimn},
  booktitle={IEEE 9th Annual Computing and Communication Workshop and Conference (CCWC 2019)},
  note={Best Paper in Track},
  year={2019}
}

@MastersThesis{Rinaldo-Ceresoli18,
    author  = {Stefano Guido Rinaldo and Andrea Ceresoli},
    title   = {Newton–Krylov–Schwarz Methods for Distributed Power Flow and Related Applications},
    school  = {Politecnico di Milano},
    year    = {2018},
    month   = {April}
}
